1 subroutine etotal(energia,fact)
2 implicit real*8 (a-h,o-z)
4 include 'DIMENSIONS.ZSCOPT'
5 include 'DIMENSIONS.FREE'
11 cMS$ATTRIBUTES C :: proc_proc
14 include 'COMMON.IOUNITS'
15 double precision energia(0:max_ene),energia1(0:max_ene+1)
21 include 'COMMON.FFIELD'
22 include 'COMMON.DERIV'
23 include 'COMMON.INTERACT'
24 include 'COMMON.SBRIDGE'
25 include 'COMMON.CHAIN'
26 include 'COMMON.CONTROL'
27 double precision fact(6)
28 cd write(iout, '(a,i2)')'Calling etotal ipot=',ipot
29 cd print *,'nnt=',nnt,' nct=',nct
31 C Compute the side-chain and electrostatic interaction energy
33 goto (101,102,103,104,105) ipot
34 C Lennard-Jones potential.
35 101 call elj(evdw,evdw_t)
36 cd print '(a)','Exit ELJ'
38 C Lennard-Jones-Kihara potential (shifted).
39 102 call eljk(evdw,evdw_t)
41 C Berne-Pechukas potential (dilated LJ, angular dependence).
42 103 call ebp(evdw,evdw_t)
44 C Gay-Berne potential (shifted LJ, angular dependence).
45 104 call egb(evdw,evdw_t)
47 C Gay-Berne-Vorobjev potential (shifted LJ, angular dependence).
48 105 call egbv(evdw,evdw_t)
50 C Calculate electrostatic (H-bonding) energy of the main chain.
52 106 call eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
54 C Calculate excluded-volume interaction energy between peptide groups
57 call escp(evdw2,evdw2_14)
59 c Calculate the bond-stretching energy
62 c write (iout,*) "estr",estr
64 C Calculate the disulfide-bridge and other energy and the contributions
65 C from other distance constraints.
66 cd print *,'Calling EHPB'
68 cd print *,'EHPB exitted succesfully.'
70 C Calculate the virtual-bond-angle energy.
73 cd print *,'Bend energy finished.'
75 C Calculate the SC local energy.
78 cd print *,'SCLOC energy finished.'
80 C Calculate the virtual-bond torsional energy.
82 cd print *,'nterm=',nterm
83 call etor(etors,edihcnstr,fact(1))
85 C 6/23/01 Calculate double-torsional energy
87 call etor_d(etors_d,fact(2))
89 C 21/5/07 Calculate local sicdechain correlation energy
91 call eback_sc_corr(esccor)
93 C 12/1/95 Multi-body terms
97 if (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0
98 & .or. wturn6.gt.0.0d0) then
99 c print *,"calling multibody_eello"
100 call multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,n_corr1)
101 c write (*,*) 'n_corr=',n_corr,' n_corr1=',n_corr1
102 c print *,ecorr,ecorr5,ecorr6,eturn6
104 if (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) then
105 call multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
109 c write(iout,*) "TEST_ENE1 constr_homology=",constr_homology
110 if (constr_homology.ge.1) then
111 call e_modeller(ehomology_constr)
113 ehomology_constr=0.0d0
116 c write(iout,*) "TEST_ENE1 ehomology_constr=",ehomology_constr
118 C BARTEK for dfa test!
119 if (wdfa_dist.gt.0) call edfad(edfadis)
120 c write(iout,*)'edfad is finished!', wdfa_dist,edfadis
121 if (wdfa_tor.gt.0) call edfat(edfator)
122 c write(iout,*)'edfat is finished!', wdfa_tor,edfator
123 if (wdfa_nei.gt.0) call edfan(edfanei)
124 c write(iout,*)'edfan is finished!', wdfa_nei,edfanei
125 if (wdfa_beta.gt.0) call edfab(edfabet)
126 c write(iout,*)'edfab is finished!', wdfa_beta,edfabet
128 c write (iout,*) "ft(6)",fact(6)," evdw",evdw," evdw_t",evdw_t
130 etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2+welec*fact(1)*ees
132 & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
133 & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
134 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
135 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
136 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
137 & +wbond*estr+wsccor*fact(1)*esccor!+ehomology_constr
138 & +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
141 etot=wsc*(evdw+fact(6)*evdw_t)+wscp*evdw2
142 & +welec*fact(1)*(ees+evdw1)
143 & +wang*ebe+wtor*fact(1)*etors+wscloc*escloc
144 & +wstrain*ehpb+wcorr*fact(3)*ecorr+wcorr5*fact(4)*ecorr5
145 & +wcorr6*fact(5)*ecorr6+wturn4*fact(3)*eello_turn4
146 & +wturn3*fact(2)*eello_turn3+wturn6*fact(5)*eturn6
147 & +wel_loc*fact(2)*eel_loc+edihcnstr+wtor_d*fact(2)*etors_d
148 & +wbond*estr+wsccor*fact(1)*esccor!+ehomology_constr
149 & +wdfa_dist*edfadis+wdfa_tor*edfator+wdfa_nei*edfanei
155 energia(2)=evdw2-evdw2_14
172 energia(8)=eello_turn3
173 energia(9)=eello_turn4
182 energia(20)=edihcnstr
184 energia(22)=ehomology_constr
189 c if (dyn_ss) call dyn_set_nss
193 if (isnan(etot).ne.0) energia(0)=1.0d+99
195 if (isnan(etot)) energia(0)=1.0d+99
200 idumm=proc_proc(etot,i)
202 call proc_proc(etot,i)
204 if(i.eq.1)energia(0)=1.0d+99
211 C Sum up the components of the Cartesian gradient.
216 gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+
217 & welec*fact(1)*gelc(j,i)+wvdwpp*gvdwpp(j,i)+
219 & wstrain*ghpbc(j,i)+
220 & wcorr*fact(3)*gradcorr(j,i)+
221 & wel_loc*fact(2)*gel_loc(j,i)+
222 & wturn3*fact(2)*gcorr3_turn(j,i)+
223 & wturn4*fact(3)*gcorr4_turn(j,i)+
224 & wcorr5*fact(4)*gradcorr5(j,i)+
225 & wcorr6*fact(5)*gradcorr6(j,i)+
226 & wturn6*fact(5)*gcorr6_turn(j,i)+
227 & wsccor*fact(2)*gsccorc(j,i)+
228 & wdfa_dist*gdfad(j,i)+
229 & wdfa_tor*gdfat(j,i)+
230 & wdfa_nei*gdfan(j,i)+
231 & wdfa_beta*gdfab(j,i)
232 gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
234 & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
235 & wsccor*fact(2)*gsccorx(j,i)
240 gradc(j,i,icg)=wsc*gvdwc(j,i)+wscp*gvdwc_scp(j,i)+
241 & welec*fact(1)*gelc(j,i)+wstrain*ghpbc(j,i)+
243 & wcorr*fact(3)*gradcorr(j,i)+
244 & wel_loc*fact(2)*gel_loc(j,i)+
245 & wturn3*fact(2)*gcorr3_turn(j,i)+
246 & wturn4*fact(3)*gcorr4_turn(j,i)+
247 & wcorr5*fact(4)*gradcorr5(j,i)+
248 & wcorr6*fact(5)*gradcorr6(j,i)+
249 & wturn6*fact(5)*gcorr6_turn(j,i)+
250 & wsccor*fact(2)*gsccorc(j,i)+
251 & wdfa_dist*gdfad(j,i)+
252 & wdfa_tor*gdfat(j,i)+
253 & wdfa_nei*gdfan(j,i)+
254 & wdfa_beta*gdfab(j,i)
255 gradx(j,i,icg)=wsc*gvdwx(j,i)+wscp*gradx_scp(j,i)+
257 & wstrain*ghpbx(j,i)+wcorr*gradxorr(j,i)+
258 & wsccor*fact(1)*gsccorx(j,i)
265 gloc(i,icg)=gloc(i,icg)+wcorr*fact(3)*gcorr_loc(i)
266 & +wcorr5*fact(4)*g_corr5_loc(i)
267 & +wcorr6*fact(5)*g_corr6_loc(i)
268 & +wturn4*fact(3)*gel_loc_turn4(i)
269 & +wturn3*fact(2)*gel_loc_turn3(i)
270 & +wturn6*fact(5)*gel_loc_turn6(i)
271 & +wel_loc*fact(2)*gel_loc_loc(i)
272 & +wsccor*fact(1)*gsccor_loc(i)
277 C------------------------------------------------------------------------
278 subroutine enerprint(energia,fact)
279 implicit real*8 (a-h,o-z)
281 include 'DIMENSIONS.ZSCOPT'
282 include 'COMMON.IOUNITS'
283 include 'COMMON.FFIELD'
284 include 'COMMON.SBRIDGE'
285 double precision energia(0:max_ene),fact(6)
287 evdw=energia(1)+fact(6)*energia(21)
289 evdw2=energia(2)+energia(17)
301 eello_turn3=energia(8)
302 eello_turn4=energia(9)
303 eello_turn6=energia(10)
310 edihcnstr=energia(20)
312 ehomology_constr=energia(22)
318 write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),evdw1,
320 & estr,wbond,ebe,wang,escloc,wscloc,etors,wtor*fact(1),
321 & etors_d,wtor_d*fact(2),ehpb,wstrain,
322 & ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),ecorr6,wcorr6*fact(5),
323 & eel_loc,wel_loc*fact(2),eello_turn3,wturn3*fact(2),
324 & eello_turn4,wturn4*fact(3),eello_turn6,wturn6*fact(5),
325 & esccor,wsccor*fact(1),edihcnstr,ehomology_constr,ebr*nss,
326 & edfadis,wdfa_dist,edfator,wdfa_tor,edfanei,wdfa_nei,edfabet,
328 10 format (/'Virtual-chain energies:'//
329 & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
330 & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
331 & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p elec)'/
332 & 'EVDWPP=',1pE16.6,' WEIGHT=',1pD16.6,' (p-p VDW)'/
333 & 'ESTR= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/
334 & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/
335 & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
336 & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
337 & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
338 & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6,
339 & ' (SS bridges & dist. cnstr.)'/
340 & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
341 & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
342 & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
343 & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/
344 & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/
345 & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/
346 & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
347 & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
348 & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
349 & 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/
350 & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
351 & 'EDFAD= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA distance energy)'/
352 & 'EDFAT= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA torsion energy)'/
353 & 'EDFAN= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA NCa energy)'/
354 & 'EDFAB= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA Beta energy)'/
355 & 'ETOT= ',1pE16.6,' (total)')
357 write (iout,10) evdw,wsc,evdw2,wscp,ees,welec*fact(1),estr,wbond,
358 & ebe,wang,escloc,wscloc,etors,wtor*fact(1),etors_d,wtor_d*fact2,
359 & ehpb,wstrain,ecorr,wcorr*fact(3),ecorr5,wcorr5*fact(4),
360 & ecorr6,wcorr6*fact(5),eel_loc,wel_loc*fact(2),
361 & eello_turn3,wturn3*fact(2),eello_turn4,wturn4*fact(3),
362 & eello_turn6,wturn6*fact(5),esccor*fact(1),wsccor,
363 & edihcnstr,ehomology_constr,ebr*nss,
364 & edfadis,wdfa_dist,edfator,wdfa_tor,edfanei,wdfa_nei,edfabet,
366 10 format (/'Virtual-chain energies:'//
367 & 'EVDW= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-SC)'/
368 & 'EVDW2= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC-p)'/
369 & 'EES= ',1pE16.6,' WEIGHT=',1pD16.6,' (p-p)'/
370 & 'ESTR= ',1pE16.6,' WEIGHT=',1pD16.6,' (stretching)'/
371 & 'EBE= ',1pE16.6,' WEIGHT=',1pD16.6,' (bending)'/
372 & 'ESC= ',1pE16.6,' WEIGHT=',1pD16.6,' (SC local)'/
373 & 'ETORS= ',1pE16.6,' WEIGHT=',1pD16.6,' (torsional)'/
374 & 'ETORSD=',1pE16.6,' WEIGHT=',1pD16.6,' (double torsional)'/
375 & 'EHBP= ',1pE16.6,' WEIGHT=',1pD16.6,
376 & ' (SS bridges & dist. cnstr.)'/
377 & 'ECORR4=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
378 & 'ECORR5=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
379 & 'ECORR6=',1pE16.6,' WEIGHT=',1pD16.6,' (multi-body)'/
380 & 'EELLO= ',1pE16.6,' WEIGHT=',1pD16.6,' (electrostatic-local)'/
381 & 'ETURN3=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 3rd order)'/
382 & 'ETURN4=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 4th order)'/
383 & 'ETURN6=',1pE16.6,' WEIGHT=',1pD16.6,' (turns, 6th order)'/
384 & 'ESCCOR=',1pE16.6,' WEIGHT=',1pD16.6,' (backbone-rotamer corr)'/
385 & 'EDIHC= ',1pE16.6,' (dihedral angle constraints)'/
386 & 'H_CONS=',1pE16.6,' (Homology model constraints energy)'/
387 & 'ESS= ',1pE16.6,' (disulfide-bridge intrinsic energy)'/
388 & 'EDFAD= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA distance energy)'/
389 & 'EDFAT= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA torsion energy)'/
390 & 'EDFAN= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA NCa energy)'/
391 & 'EDFAB= ',1pE16.6,' WEIGHT=',1pD16.6,' (DFA Beta energy)'/
392 & 'ETOT= ',1pE16.6,' (total)')
396 C-----------------------------------------------------------------------
397 subroutine elj(evdw,evdw_t)
399 C This subroutine calculates the interaction energy of nonbonded side chains
400 C assuming the LJ potential of interaction.
402 implicit real*8 (a-h,o-z)
404 include 'DIMENSIONS.ZSCOPT'
405 include "DIMENSIONS.COMPAR"
406 parameter (accur=1.0d-10)
409 include 'COMMON.LOCAL'
410 include 'COMMON.CHAIN'
411 include 'COMMON.DERIV'
412 include 'COMMON.INTERACT'
413 include 'COMMON.TORSION'
414 include 'COMMON.ENEPS'
415 include 'COMMON.SBRIDGE'
416 include 'COMMON.NAMES'
417 include 'COMMON.IOUNITS'
418 include 'COMMON.CONTACTS'
422 cd print *,'Entering ELJ nnt=',nnt,' nct=',nct,' expon=',expon
425 eneps_temp(j,i)=0.0d0
439 C Calculate SC interaction energy.
442 cd write (iout,*) 'i=',i,' iint=',iint,' istart=',istart(i,iint),
443 cd & 'iend=',iend(i,iint)
444 do j=istart(i,iint),iend(i,iint)
449 C Change 12/1/95 to calculate four-body interactions
450 rij=xj*xj+yj*yj+zj*zj
452 c write (iout,*)'i=',i,' j=',j,' itypi=',itypi,' itypj=',itypj
453 eps0ij=eps(itypi,itypj)
455 e1=fac*fac*aa(itypi,itypj)
456 e2=fac*bb(itypi,itypj)
458 ij=icant(itypi,itypj)
459 eneps_temp(1,ij)=eneps_temp(1,ij)+e1/dabs(eps0ij)
460 eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps0ij
461 cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
462 cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
463 cd write (iout,'(2(a3,i3,2x),6(1pd12.4)/2(3(1pd12.4),5x)/)')
464 cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
465 cd & bb(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,epsi,sigm,
466 cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
467 if (bb(itypi,itypj).gt.0.0d0) then
474 C Calculate the components of the gradient in DC and X
476 fac=-rrij*(e1+evdwij)
481 gvdwx(k,i)=gvdwx(k,i)-gg(k)
482 gvdwx(k,j)=gvdwx(k,j)+gg(k)
486 gvdwc(l,k)=gvdwc(l,k)+gg(l)
491 C 12/1/95, revised on 5/20/97
493 C Calculate the contact function. The ith column of the array JCONT will
494 C contain the numbers of atoms that make contacts with the atom I (of numbers
495 C greater than I). The arrays FACONT and GACONT will contain the values of
496 C the contact function and its derivative.
498 C Uncomment next line, if the correlation interactions include EVDW explicitly.
499 c if (j.gt.i+1 .and. evdwij.le.0.0D0) then
500 C Uncomment next line, if the correlation interactions are contact function only
501 if (j.gt.i+1.and. eps0ij.gt.0.0D0) then
503 sigij=sigma(itypi,itypj)
504 r0ij=rs0(itypi,itypj)
506 C Check whether the SC's are not too far to make a contact.
509 call gcont(rij,rcut,1.0d0,0.2d0*rcut,fcont,fprimcont)
510 C Add a new contact, if the SC's are close enough, but not too close (r<sigma).
512 if (fcont.gt.0.0D0) then
513 C If the SC-SC distance if close to sigma, apply spline.
514 cAdam call gcont(-rij,-1.03d0*sigij,2.0d0*sigij,1.0d0,
515 cAdam & fcont1,fprimcont1)
516 cAdam fcont1=1.0d0-fcont1
517 cAdam if (fcont1.gt.0.0d0) then
518 cAdam fprimcont=fprimcont*fcont1+fcont*fprimcont1
519 cAdam fcont=fcont*fcont1
521 C Uncomment following 4 lines to have the geometric average of the epsilon0's
522 cga eps0ij=1.0d0/dsqrt(eps0ij)
524 cga gg(k)=gg(k)*eps0ij
526 cga eps0ij=-evdwij*eps0ij
527 C Uncomment for AL's type of SC correlation interactions.
529 num_conti=num_conti+1
531 facont(num_conti,i)=fcont*eps0ij
532 fprimcont=eps0ij*fprimcont/rij
534 cAdam gacont(1,num_conti,i)=-fprimcont*xj+fcont*gg(1)
535 cAdam gacont(2,num_conti,i)=-fprimcont*yj+fcont*gg(2)
536 cAdam gacont(3,num_conti,i)=-fprimcont*zj+fcont*gg(3)
537 C Uncomment following 3 lines for Skolnick's type of SC correlation.
538 gacont(1,num_conti,i)=-fprimcont*xj
539 gacont(2,num_conti,i)=-fprimcont*yj
540 gacont(3,num_conti,i)=-fprimcont*zj
541 cd write (iout,'(2i5,2f10.5)') i,j,rij,facont(num_conti,i)
542 cd write (iout,'(2i3,3f10.5)')
543 cd & i,j,(gacont(kk,num_conti,i),kk=1,3)
549 num_cont(i)=num_conti
554 gvdwc(j,i)=expon*gvdwc(j,i)
555 gvdwx(j,i)=expon*gvdwx(j,i)
559 C******************************************************************************
563 C To save time, the factor of EXPON has been extracted from ALL components
564 C of GVDWC and GRADX. Remember to multiply them by this factor before further
567 C******************************************************************************
570 C-----------------------------------------------------------------------------
571 subroutine eljk(evdw,evdw_t)
573 C This subroutine calculates the interaction energy of nonbonded side chains
574 C assuming the LJK potential of interaction.
576 implicit real*8 (a-h,o-z)
578 include 'DIMENSIONS.ZSCOPT'
579 include "DIMENSIONS.COMPAR"
582 include 'COMMON.LOCAL'
583 include 'COMMON.CHAIN'
584 include 'COMMON.DERIV'
585 include 'COMMON.INTERACT'
586 include 'COMMON.ENEPS'
587 include 'COMMON.IOUNITS'
588 include 'COMMON.NAMES'
593 c print *,'Entering ELJK nnt=',nnt,' nct=',nct,' expon=',expon
596 eneps_temp(j,i)=0.0d0
608 C Calculate SC interaction energy.
611 do j=istart(i,iint),iend(i,iint)
616 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
618 e_augm=augm(itypi,itypj)*fac_augm
621 r_shift_inv=1.0D0/(rij+r0(itypi,itypj)-sigma(itypi,itypj))
622 fac=r_shift_inv**expon
623 e1=fac*fac*aa(itypi,itypj)
624 e2=fac*bb(itypi,itypj)
626 ij=icant(itypi,itypj)
627 eneps_temp(1,ij)=eneps_temp(1,ij)+(e1+a_augm)
628 & /dabs(eps(itypi,itypj))
629 eneps_temp(2,ij)=eneps_temp(2,ij)+e2/eps(itypi,itypj)
630 cd sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
631 cd epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
632 cd write (iout,'(2(a3,i3,2x),8(1pd12.4)/2(3(1pd12.4),5x)/)')
633 cd & restyp(itypi),i,restyp(itypj),j,aa(itypi,itypj),
634 cd & bb(itypi,itypj),augm(itypi,itypj),epsi,sigm,
635 cd & sigma(itypi,itypj),1.0D0/dsqrt(rrij),evdwij,
636 cd & (c(k,i),k=1,3),(c(k,j),k=1,3)
637 if (bb(itypi,itypj).gt.0.0d0) then
644 C Calculate the components of the gradient in DC and X
646 fac=-2.0D0*rrij*e_augm-r_inv_ij*r_shift_inv*(e1+e1+e2)
651 gvdwx(k,i)=gvdwx(k,i)-gg(k)
652 gvdwx(k,j)=gvdwx(k,j)+gg(k)
656 gvdwc(l,k)=gvdwc(l,k)+gg(l)
666 gvdwc(j,i)=expon*gvdwc(j,i)
667 gvdwx(j,i)=expon*gvdwx(j,i)
673 C-----------------------------------------------------------------------------
674 subroutine ebp(evdw,evdw_t)
676 C This subroutine calculates the interaction energy of nonbonded side chains
677 C assuming the Berne-Pechukas potential of interaction.
679 implicit real*8 (a-h,o-z)
681 include 'DIMENSIONS.ZSCOPT'
682 include "DIMENSIONS.COMPAR"
685 include 'COMMON.LOCAL'
686 include 'COMMON.CHAIN'
687 include 'COMMON.DERIV'
688 include 'COMMON.NAMES'
689 include 'COMMON.INTERACT'
690 include 'COMMON.ENEPS'
691 include 'COMMON.IOUNITS'
692 include 'COMMON.CALC'
694 c double precision rrsave(maxdim)
700 eneps_temp(j,i)=0.0d0
705 c print *,'Entering EBP nnt=',nnt,' nct=',nct,' expon=',expon
706 c if (icall.eq.0) then
718 dxi=dc_norm(1,nres+i)
719 dyi=dc_norm(2,nres+i)
720 dzi=dc_norm(3,nres+i)
721 dsci_inv=vbld_inv(i+nres)
723 C Calculate SC interaction energy.
726 do j=istart(i,iint),iend(i,iint)
729 dscj_inv=vbld_inv(j+nres)
730 chi1=chi(itypi,itypj)
731 chi2=chi(itypj,itypi)
738 alf12=0.5D0*(alf1+alf2)
739 C For diagnostics only!!!
752 dxj=dc_norm(1,nres+j)
753 dyj=dc_norm(2,nres+j)
754 dzj=dc_norm(3,nres+j)
755 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
756 cd if (icall.eq.0) then
762 C Calculate the angle-dependent terms of energy & contributions to derivatives.
764 C Calculate whole angle-dependent part of epsilon and contributions
766 fac=(rrij*sigsq)**expon2
767 e1=fac*fac*aa(itypi,itypj)
768 e2=fac*bb(itypi,itypj)
769 evdwij=eps1*eps2rt*eps3rt*(e1+e2)
770 eps2der=evdwij*eps3rt
771 eps3der=evdwij*eps2rt
772 evdwij=evdwij*eps2rt*eps3rt
773 ij=icant(itypi,itypj)
774 aux=eps1*eps2rt**2*eps3rt**2
775 eneps_temp(1,ij)=eneps_temp(1,ij)+e1*aux
776 & /dabs(eps(itypi,itypj))
777 eneps_temp(2,ij)=eneps_temp(2,ij)+e2*aux/eps(itypi,itypj)
778 if (bb(itypi,itypj).gt.0.0d0) then
785 sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
786 epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
787 cd write (iout,'(2(a3,i3,2x),15(0pf7.3))')
788 cd & restyp(itypi),i,restyp(itypj),j,
789 cd & epsi,sigm,chi1,chi2,chip1,chip2,
790 cd & eps1,eps2rt**2,eps3rt**2,1.0D0/dsqrt(sigsq),
791 cd & om1,om2,om12,1.0D0/dsqrt(rrij),
794 C Calculate gradient components.
795 e1=e1*eps1*eps2rt**2*eps3rt**2
796 fac=-expon*(e1+evdwij)
799 C Calculate radial part of the gradient
803 C Calculate the angular part of the gradient and sum add the contributions
804 C to the appropriate components of the Cartesian gradient.
813 C-----------------------------------------------------------------------------
814 subroutine egb(evdw,evdw_t)
816 C This subroutine calculates the interaction energy of nonbonded side chains
817 C assuming the Gay-Berne potential of interaction.
819 implicit real*8 (a-h,o-z)
821 include 'DIMENSIONS.ZSCOPT'
822 include "DIMENSIONS.COMPAR"
825 include 'COMMON.LOCAL'
826 include 'COMMON.CHAIN'
827 include 'COMMON.DERIV'
828 include 'COMMON.NAMES'
829 include 'COMMON.INTERACT'
830 include 'COMMON.ENEPS'
831 include 'COMMON.IOUNITS'
832 include 'COMMON.CALC'
833 include 'COMMON.SBRIDGE'
840 eneps_temp(j,i)=0.0d0
843 c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
847 c if (icall.gt.0) lprn=.true.
855 dxi=dc_norm(1,nres+i)
856 dyi=dc_norm(2,nres+i)
857 dzi=dc_norm(3,nres+i)
858 dsci_inv=vbld_inv(i+nres)
860 C Calculate SC interaction energy.
863 do j=istart(i,iint),iend(i,iint)
864 C in case of diagnostics write (iout,*) "TU SZUKAJ",i,j,dyn_ss_mask(i),dyn_ss_mask(j)
865 C /06/28/2013 Adasko: In case of dyn_ss - dynamic disulfide bond
866 C formation no electrostatic interactions should be calculated. If it
867 C would be allowed NaN would appear
868 IF (dyn_ss_mask(i).and.dyn_ss_mask(j)) THEN
869 C /06/28/2013 Adasko: dyn_ss_mask is logical statement wheather this Cys
870 C residue can or cannot form disulfide bond. There is still bug allowing
871 C Cys...Cys...Cys bond formation
872 call dyn_ssbond_ene(i,j,evdwij)
873 C /06/28/2013 Adasko: dyn_ssbond_ene is dynamic SS bond foration energy
876 c if (energy_dec) write (iout,'(a6,2i5,0pf7.3,a3)')
877 c & 'evdw',i,j,evdwij,' ss'
881 dscj_inv=vbld_inv(j+nres)
882 sig0ij=sigma(itypi,itypj)
883 chi1=chi(itypi,itypj)
884 chi2=chi(itypj,itypi)
891 alf12=0.5D0*(alf1+alf2)
892 C For diagnostics only!!!
905 dxj=dc_norm(1,nres+j)
906 dyj=dc_norm(2,nres+j)
907 dzj=dc_norm(3,nres+j)
908 c write (iout,*) i,j,xj,yj,zj
909 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
911 C Calculate angle-dependent terms of energy and contributions to their
915 sig=sig0ij*dsqrt(sigsq)
916 rij_shift=1.0D0/rij-sig+sig0ij
917 C I hate to put IF's in the loops, but here don't have another choice!!!!
918 if (rij_shift.le.0.0D0) then
923 c---------------------------------------------------------------
924 rij_shift=1.0D0/rij_shift
926 e1=fac*fac*aa(itypi,itypj)
927 e2=fac*bb(itypi,itypj)
928 evdwij=eps1*eps2rt*eps3rt*(e1+e2)
929 eps2der=evdwij*eps3rt
930 eps3der=evdwij*eps2rt
931 evdwij=evdwij*eps2rt*eps3rt
932 if (bb(itypi,itypj).gt.0) then
937 ij=icant(itypi,itypj)
938 aux=eps1*eps2rt**2*eps3rt**2
939 eneps_temp(1,ij)=eneps_temp(1,ij)+aux*e1
940 & /dabs(eps(itypi,itypj))
941 eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
942 c write (iout,*) "i",i," j",j," itypi",itypi," itypj",itypj,
943 c & " ij",ij," eneps",aux*e1/dabs(eps(itypi,itypj)),
944 c & aux*e2/eps(itypi,itypj)
945 c write (iout,'(a6,2i5,0pf7.3)') 'evdw',i,j,evdwij
947 sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
948 epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
949 write (iout,'(2(a3,i3,2x),17(0pf7.3))')
950 & restyp(itypi),i,restyp(itypj),j,
951 & epsi,sigm,chi1,chi2,chip1,chip2,
952 & eps1,eps2rt**2,eps3rt**2,sig,sig0ij,
953 & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
957 C Calculate gradient components.
958 e1=e1*eps1*eps2rt**2*eps3rt**2
959 fac=-expon*(e1+evdwij)*rij_shift
962 C Calculate the radial part of the gradient
966 C Calculate angular part of the gradient.
975 C-----------------------------------------------------------------------------
976 subroutine egbv(evdw,evdw_t)
978 C This subroutine calculates the interaction energy of nonbonded side chains
979 C assuming the Gay-Berne-Vorobjev potential of interaction.
981 implicit real*8 (a-h,o-z)
983 include 'DIMENSIONS.ZSCOPT'
984 include "DIMENSIONS.COMPAR"
987 include 'COMMON.LOCAL'
988 include 'COMMON.CHAIN'
989 include 'COMMON.DERIV'
990 include 'COMMON.NAMES'
991 include 'COMMON.INTERACT'
992 include 'COMMON.ENEPS'
993 include 'COMMON.IOUNITS'
994 include 'COMMON.CALC'
1001 eneps_temp(j,i)=0.0d0
1006 c print *,'Entering EGB nnt=',nnt,' nct=',nct,' expon=',expon
1009 c if (icall.gt.0) lprn=.true.
1011 do i=iatsc_s,iatsc_e
1017 dxi=dc_norm(1,nres+i)
1018 dyi=dc_norm(2,nres+i)
1019 dzi=dc_norm(3,nres+i)
1020 dsci_inv=vbld_inv(i+nres)
1022 C Calculate SC interaction energy.
1024 do iint=1,nint_gr(i)
1025 do j=istart(i,iint),iend(i,iint)
1028 dscj_inv=vbld_inv(j+nres)
1029 sig0ij=sigma(itypi,itypj)
1030 r0ij=r0(itypi,itypj)
1031 chi1=chi(itypi,itypj)
1032 chi2=chi(itypj,itypi)
1039 alf12=0.5D0*(alf1+alf2)
1040 C For diagnostics only!!!
1053 dxj=dc_norm(1,nres+j)
1054 dyj=dc_norm(2,nres+j)
1055 dzj=dc_norm(3,nres+j)
1056 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
1058 C Calculate angle-dependent terms of energy and contributions to their
1062 sig=sig0ij*dsqrt(sigsq)
1063 rij_shift=1.0D0/rij-sig+r0ij
1064 C I hate to put IF's in the loops, but here don't have another choice!!!!
1065 if (rij_shift.le.0.0D0) then
1070 c---------------------------------------------------------------
1071 rij_shift=1.0D0/rij_shift
1072 fac=rij_shift**expon
1073 e1=fac*fac*aa(itypi,itypj)
1074 e2=fac*bb(itypi,itypj)
1075 evdwij=eps1*eps2rt*eps3rt*(e1+e2)
1076 eps2der=evdwij*eps3rt
1077 eps3der=evdwij*eps2rt
1078 fac_augm=rrij**expon
1079 e_augm=augm(itypi,itypj)*fac_augm
1080 evdwij=evdwij*eps2rt*eps3rt
1081 if (bb(itypi,itypj).gt.0.0d0) then
1082 evdw=evdw+evdwij+e_augm
1084 evdw_t=evdw_t+evdwij+e_augm
1086 ij=icant(itypi,itypj)
1087 aux=eps1*eps2rt**2*eps3rt**2
1088 eneps_temp(1,ij)=eneps_temp(1,ij)+aux*(e1+e_augm)
1089 & /dabs(eps(itypi,itypj))
1090 eneps_temp(2,ij)=eneps_temp(2,ij)+aux*e2/eps(itypi,itypj)
1091 c eneps_temp(ij)=eneps_temp(ij)
1092 c & +(evdwij+e_augm)/eps(itypi,itypj)
1094 c sigm=dabs(aa(itypi,itypj)/bb(itypi,itypj))**(1.0D0/6.0D0)
1095 c epsi=bb(itypi,itypj)**2/aa(itypi,itypj)
1096 c write (iout,'(2(a3,i3,2x),17(0pf7.3))')
1097 c & restyp(itypi),i,restyp(itypj),j,
1098 c & epsi,sigm,sig,(augm(itypi,itypj)/epsi)**(1.0D0/12.0D0),
1099 c & chi1,chi2,chip1,chip2,
1100 c & eps1,eps2rt**2,eps3rt**2,
1101 c & om1,om2,om12,1.0D0/rij,1.0D0/rij_shift,
1105 C Calculate gradient components.
1106 e1=e1*eps1*eps2rt**2*eps3rt**2
1107 fac=-expon*(e1+evdwij)*rij_shift
1109 fac=rij*fac-2*expon*rrij*e_augm
1110 C Calculate the radial part of the gradient
1114 C Calculate angular part of the gradient.
1122 C-----------------------------------------------------------------------------
1123 subroutine sc_angular
1124 C Calculate eps1,eps2,eps3,sigma, and parts of their derivatives in om1,om2,
1125 C om12. Called by ebp, egb, and egbv.
1127 include 'COMMON.CALC'
1131 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
1132 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
1133 om12=dxi*dxj+dyi*dyj+dzi*dzj
1135 C Calculate eps1(om12) and its derivative in om12
1136 faceps1=1.0D0-om12*chiom12
1137 faceps1_inv=1.0D0/faceps1
1138 eps1=dsqrt(faceps1_inv)
1139 C Following variable is eps1*deps1/dom12
1140 eps1_om12=faceps1_inv*chiom12
1141 C Calculate sigma(om1,om2,om12) and the derivatives of sigma**2 in om1,om2,
1146 facsig=om1*chiom1+om2*chiom2-2.0D0*om1om2*chiom12
1147 sigsq=1.0D0-facsig*faceps1_inv
1148 sigsq_om1=(chiom1-chiom12*om2)*faceps1_inv
1149 sigsq_om2=(chiom2-chiom12*om1)*faceps1_inv
1150 sigsq_om12=-chi12*(om1om2*faceps1-om12*facsig)*faceps1_inv**2
1151 C Calculate eps2 and its derivatives in om1, om2, and om12.
1154 chipom12=chip12*om12
1155 facp=1.0D0-om12*chipom12
1157 facp1=om1*chipom1+om2*chipom2-2.0D0*om1om2*chipom12
1158 C Following variable is the square root of eps2
1159 eps2rt=1.0D0-facp1*facp_inv
1160 C Following three variables are the derivatives of the square root of eps
1161 C in om1, om2, and om12.
1162 eps2rt_om1=-4.0D0*(chipom1-chipom12*om2)*facp_inv
1163 eps2rt_om2=-4.0D0*(chipom2-chipom12*om1)*facp_inv
1164 eps2rt_om12=4.0D0*chip12*(om1om2*facp-om12*facp1)*facp_inv**2
1165 C Evaluate the "asymmetric" factor in the VDW constant, eps3
1166 eps3rt=1.0D0-alf1*om1+alf2*om2-alf12*om12
1167 C Calculate whole angle-dependent part of epsilon and contributions
1168 C to its derivatives
1171 C----------------------------------------------------------------------------
1173 implicit real*8 (a-h,o-z)
1174 include 'DIMENSIONS'
1175 include 'DIMENSIONS.ZSCOPT'
1176 include 'COMMON.CHAIN'
1177 include 'COMMON.DERIV'
1178 include 'COMMON.CALC'
1179 double precision dcosom1(3),dcosom2(3)
1180 eom1=eps2der*eps2rt_om1-2.0D0*alf1*eps3der+sigder*sigsq_om1
1181 eom2=eps2der*eps2rt_om2+2.0D0*alf2*eps3der+sigder*sigsq_om2
1182 eom12=evdwij*eps1_om12+eps2der*eps2rt_om12
1183 & -2.0D0*alf12*eps3der+sigder*sigsq_om12
1185 dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
1186 dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
1189 gg(k)=gg(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
1192 gvdwx(k,i)=gvdwx(k,i)-gg(k)
1193 & +(eom12*(dc_norm(k,nres+j)-om12*dc_norm(k,nres+i))
1194 & +eom1*(erij(k)-om1*dc_norm(k,nres+i)))*dsci_inv
1195 gvdwx(k,j)=gvdwx(k,j)+gg(k)
1196 & +(eom12*(dc_norm(k,nres+i)-om12*dc_norm(k,nres+j))
1197 & +eom2*(erij(k)-om2*dc_norm(k,nres+j)))*dscj_inv
1200 C Calculate the components of the gradient in DC and X
1204 gvdwc(l,k)=gvdwc(l,k)+gg(l)
1209 c------------------------------------------------------------------------------
1210 subroutine vec_and_deriv
1211 implicit real*8 (a-h,o-z)
1212 include 'DIMENSIONS'
1213 include 'DIMENSIONS.ZSCOPT'
1214 include 'COMMON.IOUNITS'
1215 include 'COMMON.GEO'
1216 include 'COMMON.VAR'
1217 include 'COMMON.LOCAL'
1218 include 'COMMON.CHAIN'
1219 include 'COMMON.VECTORS'
1220 include 'COMMON.DERIV'
1221 include 'COMMON.INTERACT'
1222 dimension uyder(3,3,2),uzder(3,3,2),vbld_inv_temp(2)
1223 C Compute the local reference systems. For reference system (i), the
1224 C X-axis points from CA(i) to CA(i+1), the Y axis is in the
1225 C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane.
1227 c if (i.eq.nres-1 .or. itel(i+1).eq.0) then
1228 if (i.eq.nres-1) then
1229 C Case of the last full residue
1230 C Compute the Z-axis
1231 call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
1232 costh=dcos(pi-theta(nres))
1233 fac=1.0d0/dsqrt(1.0d0-costh*costh)
1238 C Compute the derivatives of uz
1240 uzder(2,1,1)=-dc_norm(3,i-1)
1241 uzder(3,1,1)= dc_norm(2,i-1)
1242 uzder(1,2,1)= dc_norm(3,i-1)
1244 uzder(3,2,1)=-dc_norm(1,i-1)
1245 uzder(1,3,1)=-dc_norm(2,i-1)
1246 uzder(2,3,1)= dc_norm(1,i-1)
1249 uzder(2,1,2)= dc_norm(3,i)
1250 uzder(3,1,2)=-dc_norm(2,i)
1251 uzder(1,2,2)=-dc_norm(3,i)
1253 uzder(3,2,2)= dc_norm(1,i)
1254 uzder(1,3,2)= dc_norm(2,i)
1255 uzder(2,3,2)=-dc_norm(1,i)
1258 C Compute the Y-axis
1261 uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i))
1264 C Compute the derivatives of uy
1267 uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i)
1268 & -dc_norm(k,i)*dc_norm(j,i-1)
1269 uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
1271 uyder(j,j,1)=uyder(j,j,1)-costh
1272 uyder(j,j,2)=1.0d0+uyder(j,j,2)
1277 uygrad(l,k,j,i)=uyder(l,k,j)
1278 uzgrad(l,k,j,i)=uzder(l,k,j)
1282 call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
1283 call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
1284 call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
1285 call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
1289 C Compute the Z-axis
1290 call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i))
1291 costh=dcos(pi-theta(i+2))
1292 fac=1.0d0/dsqrt(1.0d0-costh*costh)
1297 C Compute the derivatives of uz
1299 uzder(2,1,1)=-dc_norm(3,i+1)
1300 uzder(3,1,1)= dc_norm(2,i+1)
1301 uzder(1,2,1)= dc_norm(3,i+1)
1303 uzder(3,2,1)=-dc_norm(1,i+1)
1304 uzder(1,3,1)=-dc_norm(2,i+1)
1305 uzder(2,3,1)= dc_norm(1,i+1)
1308 uzder(2,1,2)= dc_norm(3,i)
1309 uzder(3,1,2)=-dc_norm(2,i)
1310 uzder(1,2,2)=-dc_norm(3,i)
1312 uzder(3,2,2)= dc_norm(1,i)
1313 uzder(1,3,2)= dc_norm(2,i)
1314 uzder(2,3,2)=-dc_norm(1,i)
1317 C Compute the Y-axis
1320 uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
1323 C Compute the derivatives of uy
1326 uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i)
1327 & -dc_norm(k,i)*dc_norm(j,i+1)
1328 uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
1330 uyder(j,j,1)=uyder(j,j,1)-costh
1331 uyder(j,j,2)=1.0d0+uyder(j,j,2)
1336 uygrad(l,k,j,i)=uyder(l,k,j)
1337 uzgrad(l,k,j,i)=uzder(l,k,j)
1341 call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
1342 call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
1343 call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
1344 call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
1350 vbld_inv_temp(1)=vbld_inv(i+1)
1351 if (i.lt.nres-1) then
1352 vbld_inv_temp(2)=vbld_inv(i+2)
1354 vbld_inv_temp(2)=vbld_inv(i)
1359 uygrad(l,k,j,i)=vbld_inv_temp(j)*uygrad(l,k,j,i)
1360 uzgrad(l,k,j,i)=vbld_inv_temp(j)*uzgrad(l,k,j,i)
1368 C-----------------------------------------------------------------------------
1369 subroutine vec_and_deriv_test
1370 implicit real*8 (a-h,o-z)
1371 include 'DIMENSIONS'
1372 include 'DIMENSIONS.ZSCOPT'
1373 include 'COMMON.IOUNITS'
1374 include 'COMMON.GEO'
1375 include 'COMMON.VAR'
1376 include 'COMMON.LOCAL'
1377 include 'COMMON.CHAIN'
1378 include 'COMMON.VECTORS'
1379 dimension uyder(3,3,2),uzder(3,3,2)
1380 C Compute the local reference systems. For reference system (i), the
1381 C X-axis points from CA(i) to CA(i+1), the Y axis is in the
1382 C CA(i)-CA(i+1)-CA(i+2) plane, and the Z axis is perpendicular to this plane.
1384 if (i.eq.nres-1) then
1385 C Case of the last full residue
1386 C Compute the Z-axis
1387 call vecpr(dc_norm(1,i),dc_norm(1,i-1),uz(1,i))
1388 costh=dcos(pi-theta(nres))
1389 fac=1.0d0/dsqrt(1.0d0-costh*costh)
1390 c write (iout,*) 'fac',fac,
1391 c & 1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
1392 fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
1396 C Compute the derivatives of uz
1398 uzder(2,1,1)=-dc_norm(3,i-1)
1399 uzder(3,1,1)= dc_norm(2,i-1)
1400 uzder(1,2,1)= dc_norm(3,i-1)
1402 uzder(3,2,1)=-dc_norm(1,i-1)
1403 uzder(1,3,1)=-dc_norm(2,i-1)
1404 uzder(2,3,1)= dc_norm(1,i-1)
1407 uzder(2,1,2)= dc_norm(3,i)
1408 uzder(3,1,2)=-dc_norm(2,i)
1409 uzder(1,2,2)=-dc_norm(3,i)
1411 uzder(3,2,2)= dc_norm(1,i)
1412 uzder(1,3,2)= dc_norm(2,i)
1413 uzder(2,3,2)=-dc_norm(1,i)
1415 C Compute the Y-axis
1417 uy(k,i)=fac*(dc_norm(k,i-1)-costh*dc_norm(k,i))
1420 facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
1421 & (scalar(dc_norm(1,i-1),dc_norm(1,i-1))**2-
1422 & scalar(dc_norm(1,i),dc_norm(1,i-1))**2))
1424 c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
1427 & dc_norm(k,i-1)*scalar(dc_norm(1,i),dc_norm(1,i))
1428 & -scalar(dc_norm(1,i),dc_norm(1,i-1))*dc_norm(k,i)
1431 c write (iout,*) 'facy',facy,
1432 c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
1433 facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
1435 uy(k,i)=facy*uy(k,i)
1437 C Compute the derivatives of uy
1440 uyder(k,j,1)=2*dc_norm(k,i-1)*dc_norm(j,i)
1441 & -dc_norm(k,i)*dc_norm(j,i-1)
1442 uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
1444 c uyder(j,j,1)=uyder(j,j,1)-costh
1445 c uyder(j,j,2)=1.0d0+uyder(j,j,2)
1446 uyder(j,j,1)=uyder(j,j,1)
1447 & -scalar(dc_norm(1,i),dc_norm(1,i-1))
1448 uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
1454 uygrad(l,k,j,i)=uyder(l,k,j)
1455 uzgrad(l,k,j,i)=uzder(l,k,j)
1459 call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
1460 call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
1461 call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
1462 call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
1465 C Compute the Z-axis
1466 call vecpr(dc_norm(1,i),dc_norm(1,i+1),uz(1,i))
1467 costh=dcos(pi-theta(i+2))
1468 fac=1.0d0/dsqrt(1.0d0-costh*costh)
1469 fac=1.0d0/dsqrt(scalar(uz(1,i),uz(1,i)))
1473 C Compute the derivatives of uz
1475 uzder(2,1,1)=-dc_norm(3,i+1)
1476 uzder(3,1,1)= dc_norm(2,i+1)
1477 uzder(1,2,1)= dc_norm(3,i+1)
1479 uzder(3,2,1)=-dc_norm(1,i+1)
1480 uzder(1,3,1)=-dc_norm(2,i+1)
1481 uzder(2,3,1)= dc_norm(1,i+1)
1484 uzder(2,1,2)= dc_norm(3,i)
1485 uzder(3,1,2)=-dc_norm(2,i)
1486 uzder(1,2,2)=-dc_norm(3,i)
1488 uzder(3,2,2)= dc_norm(1,i)
1489 uzder(1,3,2)= dc_norm(2,i)
1490 uzder(2,3,2)=-dc_norm(1,i)
1492 C Compute the Y-axis
1494 facy=1.0d0/dsqrt(scalar(dc_norm(1,i),dc_norm(1,i))*
1495 & (scalar(dc_norm(1,i+1),dc_norm(1,i+1))**2-
1496 & scalar(dc_norm(1,i),dc_norm(1,i+1))**2))
1498 c uy(k,i)=facy*(dc_norm(k,i+1)-costh*dc_norm(k,i))
1501 & dc_norm(k,i+1)*scalar(dc_norm(1,i),dc_norm(1,i))
1502 & -scalar(dc_norm(1,i),dc_norm(1,i+1))*dc_norm(k,i)
1505 c write (iout,*) 'facy',facy,
1506 c & 1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
1507 facy=1.0d0/dsqrt(scalar(uy(1,i),uy(1,i)))
1509 uy(k,i)=facy*uy(k,i)
1511 C Compute the derivatives of uy
1514 uyder(k,j,1)=2*dc_norm(k,i+1)*dc_norm(j,i)
1515 & -dc_norm(k,i)*dc_norm(j,i+1)
1516 uyder(k,j,2)=-dc_norm(j,i)*dc_norm(k,i)
1518 c uyder(j,j,1)=uyder(j,j,1)-costh
1519 c uyder(j,j,2)=1.0d0+uyder(j,j,2)
1520 uyder(j,j,1)=uyder(j,j,1)
1521 & -scalar(dc_norm(1,i),dc_norm(1,i+1))
1522 uyder(j,j,2)=scalar(dc_norm(1,i),dc_norm(1,i))
1528 uygrad(l,k,j,i)=uyder(l,k,j)
1529 uzgrad(l,k,j,i)=uzder(l,k,j)
1533 call unormderiv(uy(1,i),uyder(1,1,1),facy,uygrad(1,1,1,i))
1534 call unormderiv(uy(1,i),uyder(1,1,2),facy,uygrad(1,1,2,i))
1535 call unormderiv(uz(1,i),uzder(1,1,1),fac,uzgrad(1,1,1,i))
1536 call unormderiv(uz(1,i),uzder(1,1,2),fac,uzgrad(1,1,2,i))
1543 uygrad(l,k,j,i)=vblinv*uygrad(l,k,j,i)
1544 uzgrad(l,k,j,i)=vblinv*uzgrad(l,k,j,i)
1551 C-----------------------------------------------------------------------------
1552 subroutine check_vecgrad
1553 implicit real*8 (a-h,o-z)
1554 include 'DIMENSIONS'
1555 include 'DIMENSIONS.ZSCOPT'
1556 include 'COMMON.IOUNITS'
1557 include 'COMMON.GEO'
1558 include 'COMMON.VAR'
1559 include 'COMMON.LOCAL'
1560 include 'COMMON.CHAIN'
1561 include 'COMMON.VECTORS'
1562 dimension uygradt(3,3,2,maxres),uzgradt(3,3,2,maxres)
1563 dimension uyt(3,maxres),uzt(3,maxres)
1564 dimension uygradn(3,3,2),uzgradn(3,3,2),erij(3)
1565 double precision delta /1.0d-7/
1568 crc write(iout,'(2i5,2(3f10.5,5x))') i,1,dc_norm(:,i)
1569 crc write(iout,'(2i5,2(3f10.5,5x))') i,2,uy(:,i)
1570 crc write(iout,'(2i5,2(3f10.5,5x)/)')i,3,uz(:,i)
1571 cd write(iout,'(2i5,2(3f10.5,5x))') i,1,
1572 cd & (dc_norm(if90,i),if90=1,3)
1573 cd write(iout,'(2i5,2(3f10.5,5x))') i,2,(uy(if90,i),if90=1,3)
1574 cd write(iout,'(2i5,2(3f10.5,5x)/)')i,3,(uz(if90,i),if90=1,3)
1575 cd write(iout,'(a)')
1581 uygradt(l,k,j,i)=uygrad(l,k,j,i)
1582 uzgradt(l,k,j,i)=uzgrad(l,k,j,i)
1595 cd write (iout,*) 'i=',i
1597 erij(k)=dc_norm(k,i)
1601 dc_norm(k,i)=erij(k)
1603 dc_norm(j,i)=dc_norm(j,i)+delta
1604 c fac=dsqrt(scalar(dc_norm(1,i),dc_norm(1,i)))
1606 c dc_norm(k,i)=dc_norm(k,i)/fac
1608 c write (iout,*) (dc_norm(k,i),k=1,3)
1609 c write (iout,*) (erij(k),k=1,3)
1612 uygradn(k,j,1)=(uy(k,i)-uyt(k,i))/delta
1613 uygradn(k,j,2)=(uy(k,i-1)-uyt(k,i-1))/delta
1614 uzgradn(k,j,1)=(uz(k,i)-uzt(k,i))/delta
1615 uzgradn(k,j,2)=(uz(k,i-1)-uzt(k,i-1))/delta
1617 c write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
1618 c & j,(uzgradt(k,j,1,i),k=1,3),(uzgradn(k,j,1),k=1,3),
1619 c & (uzgradt(k,j,2,i-1),k=1,3),(uzgradn(k,j,2),k=1,3)
1622 dc_norm(k,i)=erij(k)
1625 cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
1626 cd & k,(uygradt(k,l,1,i),l=1,3),(uygradn(k,l,1),l=1,3),
1627 cd & (uygradt(k,l,2,i-1),l=1,3),(uygradn(k,l,2),l=1,3)
1628 cd write (iout,'(i5,3f8.5,3x,3f8.5,5x,3f8.5,3x,3f8.5)')
1629 cd & k,(uzgradt(k,l,1,i),l=1,3),(uzgradn(k,l,1),l=1,3),
1630 cd & (uzgradt(k,l,2,i-1),l=1,3),(uzgradn(k,l,2),l=1,3)
1631 cd write (iout,'(a)')
1636 C--------------------------------------------------------------------------
1637 subroutine set_matrices
1638 implicit real*8 (a-h,o-z)
1639 include 'DIMENSIONS'
1640 include 'DIMENSIONS.ZSCOPT'
1641 include 'COMMON.IOUNITS'
1642 include 'COMMON.GEO'
1643 include 'COMMON.VAR'
1644 include 'COMMON.LOCAL'
1645 include 'COMMON.CHAIN'
1646 include 'COMMON.DERIV'
1647 include 'COMMON.INTERACT'
1648 include 'COMMON.CONTACTS'
1649 include 'COMMON.TORSION'
1650 include 'COMMON.VECTORS'
1651 include 'COMMON.FFIELD'
1652 double precision auxvec(2),auxmat(2,2)
1654 C Compute the virtual-bond-torsional-angle dependent quantities needed
1655 C to calculate the el-loc multibody terms of various order.
1658 if (i .lt. nres+1) then
1695 if (i .gt. 3 .and. i .lt. nres+1) then
1696 obrot_der(1,i-2)=-sin1
1697 obrot_der(2,i-2)= cos1
1698 Ugder(1,1,i-2)= sin1
1699 Ugder(1,2,i-2)=-cos1
1700 Ugder(2,1,i-2)=-cos1
1701 Ugder(2,2,i-2)=-sin1
1704 obrot2_der(1,i-2)=-dwasin2
1705 obrot2_der(2,i-2)= dwacos2
1706 Ug2der(1,1,i-2)= dwasin2
1707 Ug2der(1,2,i-2)=-dwacos2
1708 Ug2der(2,1,i-2)=-dwacos2
1709 Ug2der(2,2,i-2)=-dwasin2
1711 obrot_der(1,i-2)=0.0d0
1712 obrot_der(2,i-2)=0.0d0
1713 Ugder(1,1,i-2)=0.0d0
1714 Ugder(1,2,i-2)=0.0d0
1715 Ugder(2,1,i-2)=0.0d0
1716 Ugder(2,2,i-2)=0.0d0
1717 obrot2_der(1,i-2)=0.0d0
1718 obrot2_der(2,i-2)=0.0d0
1719 Ug2der(1,1,i-2)=0.0d0
1720 Ug2der(1,2,i-2)=0.0d0
1721 Ug2der(2,1,i-2)=0.0d0
1722 Ug2der(2,2,i-2)=0.0d0
1724 if (i.gt. iatel_s+2 .and. i.lt.iatel_e+5) then
1725 iti = itortyp(itype(i-2))
1729 if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
1730 iti1 = itortyp(itype(i-1))
1734 cd write (iout,*) '*******i',i,' iti1',iti
1735 cd write (iout,*) 'b1',b1(:,iti)
1736 cd write (iout,*) 'b2',b2(:,iti)
1737 cd write (iout,*) 'Ug',Ug(:,:,i-2)
1738 if (i .gt. iatel_s+2) then
1739 call matvec2(Ug(1,1,i-2),b2(1,iti),Ub2(1,i-2))
1740 call matmat2(EE(1,1,iti),Ug(1,1,i-2),EUg(1,1,i-2))
1741 call matmat2(CC(1,1,iti),Ug(1,1,i-2),CUg(1,1,i-2))
1742 call matmat2(DD(1,1,iti),Ug(1,1,i-2),DUg(1,1,i-2))
1743 call matmat2(Dtilde(1,1,iti),Ug2(1,1,i-2),DtUg2(1,1,i-2))
1744 call matvec2(Ctilde(1,1,iti1),obrot(1,i-2),Ctobr(1,i-2))
1745 call matvec2(Dtilde(1,1,iti),obrot2(1,i-2),Dtobr2(1,i-2))
1755 DtUg2(l,k,i-2)=0.0d0
1759 call matvec2(Ugder(1,1,i-2),b2(1,iti),Ub2der(1,i-2))
1760 call matmat2(EE(1,1,iti),Ugder(1,1,i-2),EUgder(1,1,i-2))
1761 call matmat2(CC(1,1,iti1),Ugder(1,1,i-2),CUgder(1,1,i-2))
1762 call matmat2(DD(1,1,iti),Ugder(1,1,i-2),DUgder(1,1,i-2))
1763 call matmat2(Dtilde(1,1,iti),Ug2der(1,1,i-2),DtUg2der(1,1,i-2))
1764 call matvec2(Ctilde(1,1,iti1),obrot_der(1,i-2),Ctobrder(1,i-2))
1765 call matvec2(Dtilde(1,1,iti),obrot2_der(1,i-2),Dtobr2der(1,i-2))
1767 muder(k,i-2)=Ub2der(k,i-2)
1769 if (i.gt. iatel_s+1 .and. i.lt.iatel_e+4) then
1770 iti1 = itortyp(itype(i-1))
1775 mu(k,i-2)=Ub2(k,i-2)+b1(k,iti1)
1777 C Vectors and matrices dependent on a single virtual-bond dihedral.
1778 call matvec2(DD(1,1,iti),b1tilde(1,iti1),auxvec(1))
1779 call matvec2(Ug2(1,1,i-2),auxvec(1),Ug2Db1t(1,i-2))
1780 call matvec2(Ug2der(1,1,i-2),auxvec(1),Ug2Db1tder(1,i-2))
1781 call matvec2(CC(1,1,iti1),Ub2(1,i-2),CUgb2(1,i-2))
1782 call matvec2(CC(1,1,iti1),Ub2der(1,i-2),CUgb2der(1,i-2))
1783 call matmat2(EUg(1,1,i-2),CC(1,1,iti1),EUgC(1,1,i-2))
1784 call matmat2(EUgder(1,1,i-2),CC(1,1,iti1),EUgCder(1,1,i-2))
1785 call matmat2(EUg(1,1,i-2),DD(1,1,iti1),EUgD(1,1,i-2))
1786 call matmat2(EUgder(1,1,i-2),DD(1,1,iti1),EUgDder(1,1,i-2))
1787 cd write (iout,*) 'i',i,' mu ',(mu(k,i-2),k=1,2),
1788 cd & ' mu1',(b1(k,i-2),k=1,2),' mu2',(Ub2(k,i-2),k=1,2)
1790 C Matrices dependent on two consecutive virtual-bond dihedrals.
1791 C The order of matrices is from left to right.
1793 call matmat2(DtUg2(1,1,i-1),EUg(1,1,i),DtUg2EUg(1,1,i))
1794 call matmat2(DtUg2der(1,1,i-1),EUg(1,1,i),DtUg2EUgder(1,1,1,i))
1795 call matmat2(DtUg2(1,1,i-1),EUgder(1,1,i),DtUg2EUgder(1,1,2,i))
1796 call transpose2(DtUg2(1,1,i-1),auxmat(1,1))
1797 call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUg(1,1,i))
1798 call matmat2(auxmat(1,1),EUgder(1,1,i),Ug2DtEUgder(1,1,2,i))
1799 call transpose2(DtUg2der(1,1,i-1),auxmat(1,1))
1800 call matmat2(auxmat(1,1),EUg(1,1,i),Ug2DtEUgder(1,1,1,i))
1803 cd iti = itortyp(itype(i))
1806 cd write (iout,'(2f10.5,5x,2f10.5,5x,2f10.5)')
1807 cd & (EE(j,k,iti),k=1,2),(Ug(j,k,i),k=1,2),(EUg(j,k,i),k=1,2)
1812 C--------------------------------------------------------------------------
1813 subroutine eelec(ees,evdw1,eel_loc,eello_turn3,eello_turn4)
1815 C This subroutine calculates the average interaction energy and its gradient
1816 C in the virtual-bond vectors between non-adjacent peptide groups, based on
1817 C the potential described in Liwo et al., Protein Sci., 1993, 2, 1715.
1818 C The potential depends both on the distance of peptide-group centers and on
1819 C the orientation of the CA-CA virtual bonds.
1821 implicit real*8 (a-h,o-z)
1822 include 'DIMENSIONS'
1823 include 'DIMENSIONS.ZSCOPT'
1824 include 'DIMENSIONS.FREE'
1825 include 'COMMON.CONTROL'
1826 include 'COMMON.IOUNITS'
1827 include 'COMMON.GEO'
1828 include 'COMMON.VAR'
1829 include 'COMMON.LOCAL'
1830 include 'COMMON.CHAIN'
1831 include 'COMMON.DERIV'
1832 include 'COMMON.INTERACT'
1833 include 'COMMON.CONTACTS'
1834 include 'COMMON.TORSION'
1835 include 'COMMON.VECTORS'
1836 include 'COMMON.FFIELD'
1837 dimension ggg(3),gggp(3),gggm(3),erij(3),dcosb(3),dcosg(3),
1838 & erder(3,3),uryg(3,3),urzg(3,3),vryg(3,3),vrzg(3,3)
1839 double precision acipa(2,2),agg(3,4),aggi(3,4),aggi1(3,4),
1840 & aggj(3,4),aggj1(3,4),a_temp(2,2),muij(4)
1841 common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1
1842 c 4/26/02 - AL scaling factor for 1,4 repulsive VDW interactions
1843 double precision scal_el /0.5d0/
1845 C 13-go grudnia roku pamietnego...
1846 double precision unmat(3,3) /1.0d0,0.0d0,0.0d0,
1847 & 0.0d0,1.0d0,0.0d0,
1848 & 0.0d0,0.0d0,1.0d0/
1849 cd write(iout,*) 'In EELEC'
1851 cd write(iout,*) 'Type',i
1852 cd write(iout,*) 'B1',B1(:,i)
1853 cd write(iout,*) 'B2',B2(:,i)
1854 cd write(iout,*) 'CC',CC(:,:,i)
1855 cd write(iout,*) 'DD',DD(:,:,i)
1856 cd write(iout,*) 'EE',EE(:,:,i)
1858 cd call check_vecgrad
1860 if (icheckgrad.eq.1) then
1862 fac=1.0d0/dsqrt(scalar(dc(1,i),dc(1,i)))
1864 dc_norm(k,i)=dc(k,i)*fac
1866 c write (iout,*) 'i',i,' fac',fac
1869 if (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
1870 & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0 .or.
1871 & wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) then
1872 cd if (wel_loc.gt.0.0d0) then
1873 if (icheckgrad.eq.1) then
1874 call vec_and_deriv_test
1881 cd write (iout,*) 'i=',i
1883 cd write (iout,'(i5,2f10.5)') k,uy(k,i),uz(k,i)
1886 cd write (iout,'(f10.5,2x,3f10.5,2x,3f10.5)')
1887 cd & uz(k,i),(uzgrad(k,l,1,i),l=1,3),(uzgrad(k,l,2,i),l=1,3)
1900 cd print '(a)','Enter EELEC'
1901 cd write (iout,*) 'iatel_s=',iatel_s,' iatel_e=',iatel_e
1903 gel_loc_loc(i)=0.0d0
1906 do i=iatel_s,iatel_e
1907 if (itel(i).eq.0) goto 1215
1911 dx_normi=dc_norm(1,i)
1912 dy_normi=dc_norm(2,i)
1913 dz_normi=dc_norm(3,i)
1914 xmedi=c(1,i)+0.5d0*dxi
1915 ymedi=c(2,i)+0.5d0*dyi
1916 zmedi=c(3,i)+0.5d0*dzi
1918 c write (iout,*) 'i',i,' ielstart',ielstart(i),' ielend',ielend(i)
1919 do j=ielstart(i),ielend(i)
1920 if (itel(j).eq.0) goto 1216
1924 if (j.eq.i+2 .and. itelj.eq.2) iteli=2
1925 aaa=app(iteli,itelj)
1926 bbb=bpp(iteli,itelj)
1927 C Diagnostics only!!!
1933 ael6i=ael6(iteli,itelj)
1934 ael3i=ael3(iteli,itelj)
1938 dx_normj=dc_norm(1,j)
1939 dy_normj=dc_norm(2,j)
1940 dz_normj=dc_norm(3,j)
1941 xj=c(1,j)+0.5D0*dxj-xmedi
1942 yj=c(2,j)+0.5D0*dyj-ymedi
1943 zj=c(3,j)+0.5D0*dzj-zmedi
1944 rij=xj*xj+yj*yj+zj*zj
1950 cosa=dx_normi*dx_normj+dy_normi*dy_normj+dz_normi*dz_normj
1951 cosb=(xj*dx_normi+yj*dy_normi+zj*dz_normi)*rmij
1952 cosg=(xj*dx_normj+yj*dy_normj+zj*dz_normj)*rmij
1953 fac=cosa-3.0D0*cosb*cosg
1955 c 4/26/02 - AL scaling down 1,4 repulsive VDW interactions
1956 if (j.eq.i+2) ev1=scal_el*ev1
1961 el1=fac3*(4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg))
1964 c write (iout,*) "i",i,iteli," j",j,itelj," eesij",eesij
1965 C 12/26/95 - for the evaluation of multi-body H-bonding interactions
1966 ees0ij=4.0D0+fac*fac-3.0D0*(cosb*cosb+cosg*cosg)
1969 cd write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
1970 cd & iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
1971 cd & 1.0D0/dsqrt(rrmij),evdwij,eesij,
1972 cd & xmedi,ymedi,zmedi,xj,yj,zj
1974 C Calculate contributions to the Cartesian gradient.
1977 facvdw=-6*rrmij*(ev1+evdwij)
1978 facel=-3*rrmij*(el1+eesij)
1985 * Radial derivatives. First process both termini of the fragment (i,j)
1992 gelc(k,i)=gelc(k,i)+ghalf
1993 gelc(k,j)=gelc(k,j)+ghalf
1996 * Loop over residues i+1 thru j-1.
2000 gelc(l,k)=gelc(l,k)+ggg(l)
2008 gvdwpp(k,i)=gvdwpp(k,i)+ghalf
2009 gvdwpp(k,j)=gvdwpp(k,j)+ghalf
2012 * Loop over residues i+1 thru j-1.
2016 gvdwpp(l,k)=gvdwpp(l,k)+ggg(l)
2023 fac=-3*rrmij*(facvdw+facvdw+facel)
2029 * Radial derivatives. First process both termini of the fragment (i,j)
2036 gelc(k,i)=gelc(k,i)+ghalf
2037 gelc(k,j)=gelc(k,j)+ghalf
2040 * Loop over residues i+1 thru j-1.
2044 gelc(l,k)=gelc(l,k)+ggg(l)
2051 ecosa=2.0D0*fac3*fac1+fac4
2054 ecosb=(fac3*(fac1*cosg+cosb)+cosg*fac4)
2055 ecosg=(fac3*(fac1*cosb+cosg)+cosb*fac4)
2057 dcosb(k)=rmij*(dc_norm(k,i)-erij(k)*cosb)
2058 dcosg(k)=rmij*(dc_norm(k,j)-erij(k)*cosg)
2060 cd print '(2i3,2(3(1pd14.5),3x))',i,j,(dcosb(k),k=1,3),
2061 cd & (dcosg(k),k=1,3)
2063 ggg(k)=ecosb*dcosb(k)+ecosg*dcosg(k)
2067 gelc(k,i)=gelc(k,i)+ghalf
2068 & +(ecosa*(dc_norm(k,j)-cosa*dc_norm(k,i))
2069 & + ecosb*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
2070 gelc(k,j)=gelc(k,j)+ghalf
2071 & +(ecosa*(dc_norm(k,i)-cosa*dc_norm(k,j))
2072 & + ecosg*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
2076 gelc(l,k)=gelc(l,k)+ggg(l)
2081 IF (wel_loc.gt.0.0d0 .or. wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0
2082 & .or. wcorr6.gt.0.0d0 .or. wturn3.gt.0.0d0
2083 & .or. wturn4.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
2085 C 9/25/99 Mixed third-order local-electrostatic terms. The local-interaction
2086 C energy of a peptide unit is assumed in the form of a second-order
2087 C Fourier series in the angles lambda1 and lambda2 (see Nishikawa et al.
2088 C Macromolecules, 1974, 7, 797-806 for definition). This correlation terms
2089 C are computed for EVERY pair of non-contiguous peptide groups.
2091 if (j.lt.nres-1) then
2102 muij(kkk)=mu(k,i)*mu(l,j)
2105 cd write (iout,*) 'EELEC: i',i,' j',j
2106 cd write (iout,*) 'j',j,' j1',j1,' j2',j2
2107 cd write(iout,*) 'muij',muij
2108 ury=scalar(uy(1,i),erij)
2109 urz=scalar(uz(1,i),erij)
2110 vry=scalar(uy(1,j),erij)
2111 vrz=scalar(uz(1,j),erij)
2112 a22=scalar(uy(1,i),uy(1,j))-3*ury*vry
2113 a23=scalar(uy(1,i),uz(1,j))-3*ury*vrz
2114 a32=scalar(uz(1,i),uy(1,j))-3*urz*vry
2115 a33=scalar(uz(1,i),uz(1,j))-3*urz*vrz
2116 C For diagnostics only
2121 fac=dsqrt(-ael6i)*r3ij
2122 cd write (2,*) 'fac=',fac
2123 C For diagnostics only
2129 cd write (iout,'(4i5,4f10.5)')
2130 cd & i,itortyp(itype(i)),j,itortyp(itype(j)),a22,a23,a32,a33
2131 cd write (iout,'(6f10.5)') (muij(k),k=1,4),fac,eel_loc_ij
2132 cd write (iout,'(2(3f10.5,5x)/2(3f10.5,5x))') (uy(k,i),k=1,3),
2133 cd & (uz(k,i),k=1,3),(uy(k,j),k=1,3),(uz(k,j),k=1,3)
2134 cd write (iout,'(4f10.5)')
2135 cd & scalar(uy(1,i),uy(1,j)),scalar(uy(1,i),uz(1,j)),
2136 cd & scalar(uz(1,i),uy(1,j)),scalar(uz(1,i),uz(1,j))
2137 cd write (iout,'(4f10.5)') ury,urz,vry,vrz
2138 cd write (iout,'(2i3,9f10.5/)') i,j,
2139 cd & fac22,a22,fac23,a23,fac32,a32,fac33,a33,eel_loc_ij
2141 C Derivatives of the elements of A in virtual-bond vectors
2142 call unormderiv(erij(1),unmat(1,1),rmij,erder(1,1))
2149 uryg(k,1)=scalar(erder(1,k),uy(1,i))
2150 uryg(k,2)=scalar(uygrad(1,k,1,i),erij(1))
2151 uryg(k,3)=scalar(uygrad(1,k,2,i),erij(1))
2152 urzg(k,1)=scalar(erder(1,k),uz(1,i))
2153 urzg(k,2)=scalar(uzgrad(1,k,1,i),erij(1))
2154 urzg(k,3)=scalar(uzgrad(1,k,2,i),erij(1))
2155 vryg(k,1)=scalar(erder(1,k),uy(1,j))
2156 vryg(k,2)=scalar(uygrad(1,k,1,j),erij(1))
2157 vryg(k,3)=scalar(uygrad(1,k,2,j),erij(1))
2158 vrzg(k,1)=scalar(erder(1,k),uz(1,j))
2159 vrzg(k,2)=scalar(uzgrad(1,k,1,j),erij(1))
2160 vrzg(k,3)=scalar(uzgrad(1,k,2,j),erij(1))
2170 C Compute radial contributions to the gradient
2192 C Add the contributions coming from er
2195 agg(k,1)=agg(k,1)+fac3*(uryg(k,1)*vry+vryg(k,1)*ury)
2196 agg(k,2)=agg(k,2)+fac3*(uryg(k,1)*vrz+vrzg(k,1)*ury)
2197 agg(k,3)=agg(k,3)+fac3*(urzg(k,1)*vry+vryg(k,1)*urz)
2198 agg(k,4)=agg(k,4)+fac3*(urzg(k,1)*vrz+vrzg(k,1)*urz)
2201 C Derivatives in DC(i)
2202 ghalf1=0.5d0*agg(k,1)
2203 ghalf2=0.5d0*agg(k,2)
2204 ghalf3=0.5d0*agg(k,3)
2205 ghalf4=0.5d0*agg(k,4)
2206 aggi(k,1)=fac*(scalar(uygrad(1,k,1,i),uy(1,j))
2207 & -3.0d0*uryg(k,2)*vry)+ghalf1
2208 aggi(k,2)=fac*(scalar(uygrad(1,k,1,i),uz(1,j))
2209 & -3.0d0*uryg(k,2)*vrz)+ghalf2
2210 aggi(k,3)=fac*(scalar(uzgrad(1,k,1,i),uy(1,j))
2211 & -3.0d0*urzg(k,2)*vry)+ghalf3
2212 aggi(k,4)=fac*(scalar(uzgrad(1,k,1,i),uz(1,j))
2213 & -3.0d0*urzg(k,2)*vrz)+ghalf4
2214 C Derivatives in DC(i+1)
2215 aggi1(k,1)=fac*(scalar(uygrad(1,k,2,i),uy(1,j))
2216 & -3.0d0*uryg(k,3)*vry)+agg(k,1)
2217 aggi1(k,2)=fac*(scalar(uygrad(1,k,2,i),uz(1,j))
2218 & -3.0d0*uryg(k,3)*vrz)+agg(k,2)
2219 aggi1(k,3)=fac*(scalar(uzgrad(1,k,2,i),uy(1,j))
2220 & -3.0d0*urzg(k,3)*vry)+agg(k,3)
2221 aggi1(k,4)=fac*(scalar(uzgrad(1,k,2,i),uz(1,j))
2222 & -3.0d0*urzg(k,3)*vrz)+agg(k,4)
2223 C Derivatives in DC(j)
2224 aggj(k,1)=fac*(scalar(uygrad(1,k,1,j),uy(1,i))
2225 & -3.0d0*vryg(k,2)*ury)+ghalf1
2226 aggj(k,2)=fac*(scalar(uzgrad(1,k,1,j),uy(1,i))
2227 & -3.0d0*vrzg(k,2)*ury)+ghalf2
2228 aggj(k,3)=fac*(scalar(uygrad(1,k,1,j),uz(1,i))
2229 & -3.0d0*vryg(k,2)*urz)+ghalf3
2230 aggj(k,4)=fac*(scalar(uzgrad(1,k,1,j),uz(1,i))
2231 & -3.0d0*vrzg(k,2)*urz)+ghalf4
2232 C Derivatives in DC(j+1) or DC(nres-1)
2233 aggj1(k,1)=fac*(scalar(uygrad(1,k,2,j),uy(1,i))
2234 & -3.0d0*vryg(k,3)*ury)
2235 aggj1(k,2)=fac*(scalar(uzgrad(1,k,2,j),uy(1,i))
2236 & -3.0d0*vrzg(k,3)*ury)
2237 aggj1(k,3)=fac*(scalar(uygrad(1,k,2,j),uz(1,i))
2238 & -3.0d0*vryg(k,3)*urz)
2239 aggj1(k,4)=fac*(scalar(uzgrad(1,k,2,j),uz(1,i))
2240 & -3.0d0*vrzg(k,3)*urz)
2245 C Derivatives in DC(i+1)
2246 cd aggi1(k,1)=agg(k,1)
2247 cd aggi1(k,2)=agg(k,2)
2248 cd aggi1(k,3)=agg(k,3)
2249 cd aggi1(k,4)=agg(k,4)
2250 C Derivatives in DC(j)
2255 C Derivatives in DC(j+1)
2260 if (j.eq.nres-1 .and. i.lt.j-2) then
2262 aggj1(k,l)=aggj1(k,l)+agg(k,l)
2263 cd aggj1(k,l)=agg(k,l)
2269 C Check the loc-el terms by numerical integration
2279 aggi(k,l)=-aggi(k,l)
2280 aggi1(k,l)=-aggi1(k,l)
2281 aggj(k,l)=-aggj(k,l)
2282 aggj1(k,l)=-aggj1(k,l)
2285 if (j.lt.nres-1) then
2291 aggi(k,l)=-aggi(k,l)
2292 aggi1(k,l)=-aggi1(k,l)
2293 aggj(k,l)=-aggj(k,l)
2294 aggj1(k,l)=-aggj1(k,l)
2305 aggi(k,l)=-aggi(k,l)
2306 aggi1(k,l)=-aggi1(k,l)
2307 aggj(k,l)=-aggj(k,l)
2308 aggj1(k,l)=-aggj1(k,l)
2314 IF (wel_loc.gt.0.0d0) THEN
2315 C Contribution to the local-electrostatic energy coming from the i-j pair
2316 eel_loc_ij=a22*muij(1)+a23*muij(2)+a32*muij(3)
2318 cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
2319 cd write (iout,*) a22,muij(1),a23,muij(2),a32,muij(3)
2320 eel_loc=eel_loc+eel_loc_ij
2321 C Partial derivatives in virtual-bond dihedral angles gamma
2324 & gel_loc_loc(i-1)=gel_loc_loc(i-1)+
2325 & a22*muder(1,i)*mu(1,j)+a23*muder(1,i)*mu(2,j)
2326 & +a32*muder(2,i)*mu(1,j)+a33*muder(2,i)*mu(2,j)
2327 gel_loc_loc(j-1)=gel_loc_loc(j-1)+
2328 & a22*mu(1,i)*muder(1,j)+a23*mu(1,i)*muder(2,j)
2329 & +a32*mu(2,i)*muder(1,j)+a33*mu(2,i)*muder(2,j)
2330 cd call checkint3(i,j,mu1,mu2,a22,a23,a32,a33,acipa,eel_loc_ij)
2331 cd write(iout,*) 'agg ',agg
2332 cd write(iout,*) 'aggi ',aggi
2333 cd write(iout,*) 'aggi1',aggi1
2334 cd write(iout,*) 'aggj ',aggj
2335 cd write(iout,*) 'aggj1',aggj1
2337 C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
2339 ggg(l)=agg(l,1)*muij(1)+
2340 & agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)
2344 gel_loc(l,k)=gel_loc(l,k)+ggg(l)
2347 C Remaining derivatives of eello
2349 gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+
2350 & aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)
2351 gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+
2352 & aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)
2353 gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+
2354 & aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)
2355 gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+
2356 & aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)
2360 if (wturn3.gt.0.0d0 .or. wturn4.gt.0.0d0) then
2361 C Contributions from turns
2366 call eturn34(i,j,eello_turn3,eello_turn4)
2368 C Change 12/26/95 to calculate four-body contributions to H-bonding energy
2369 if (j.gt.i+1 .and. num_conti.le.maxconts) then
2371 C Calculate the contact function. The ith column of the array JCONT will
2372 C contain the numbers of atoms that make contacts with the atom I (of numbers
2373 C greater than I). The arrays FACONT and GACONT will contain the values of
2374 C the contact function and its derivative.
2375 c r0ij=1.02D0*rpp(iteli,itelj)
2376 c r0ij=1.11D0*rpp(iteli,itelj)
2377 r0ij=2.20D0*rpp(iteli,itelj)
2378 c r0ij=1.55D0*rpp(iteli,itelj)
2379 call gcont(rij,r0ij,1.0D0,0.2d0*r0ij,fcont,fprimcont)
2380 if (fcont.gt.0.0D0) then
2381 num_conti=num_conti+1
2382 if (num_conti.gt.maxconts) then
2383 write (iout,*) 'WARNING - max. # of contacts exceeded;',
2384 & ' will skip next contacts for this conf.'
2386 jcont_hb(num_conti,i)=j
2387 IF (wcorr4.gt.0.0d0 .or. wcorr5.gt.0.0d0 .or.
2388 & wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) THEN
2389 C 9/30/99 (AL) - store components necessary to evaluate higher-order loc-el
2391 d_cont(num_conti,i)=rij
2392 cd write (2,'(3e15.5)') rij,r0ij+0.2d0*r0ij,rij
2393 C --- Electrostatic-interaction matrix ---
2394 a_chuj(1,1,num_conti,i)=a22
2395 a_chuj(1,2,num_conti,i)=a23
2396 a_chuj(2,1,num_conti,i)=a32
2397 a_chuj(2,2,num_conti,i)=a33
2398 C --- Gradient of rij
2400 grij_hb_cont(kkk,num_conti,i)=erij(kkk)
2403 c a_chuj(1,1,num_conti,i)=-0.61d0
2404 c a_chuj(1,2,num_conti,i)= 0.4d0
2405 c a_chuj(2,1,num_conti,i)= 0.65d0
2406 c a_chuj(2,2,num_conti,i)= 0.50d0
2407 c else if (i.eq.2) then
2408 c a_chuj(1,1,num_conti,i)= 0.0d0
2409 c a_chuj(1,2,num_conti,i)= 0.0d0
2410 c a_chuj(2,1,num_conti,i)= 0.0d0
2411 c a_chuj(2,2,num_conti,i)= 0.0d0
2413 C --- and its gradients
2414 cd write (iout,*) 'i',i,' j',j
2416 cd write (iout,*) 'iii 1 kkk',kkk
2417 cd write (iout,*) agg(kkk,:)
2420 cd write (iout,*) 'iii 2 kkk',kkk
2421 cd write (iout,*) aggi(kkk,:)
2424 cd write (iout,*) 'iii 3 kkk',kkk
2425 cd write (iout,*) aggi1(kkk,:)
2428 cd write (iout,*) 'iii 4 kkk',kkk
2429 cd write (iout,*) aggj(kkk,:)
2432 cd write (iout,*) 'iii 5 kkk',kkk
2433 cd write (iout,*) aggj1(kkk,:)
2440 a_chuj_der(k,l,m,1,num_conti,i)=agg(m,kkll)
2441 a_chuj_der(k,l,m,2,num_conti,i)=aggi(m,kkll)
2442 a_chuj_der(k,l,m,3,num_conti,i)=aggi1(m,kkll)
2443 a_chuj_der(k,l,m,4,num_conti,i)=aggj(m,kkll)
2444 a_chuj_der(k,l,m,5,num_conti,i)=aggj1(m,kkll)
2446 c a_chuj_der(k,l,m,mm,num_conti,i)=0.0d0
2452 IF (wcorr4.eq.0.0d0 .and. wcorr.gt.0.0d0) THEN
2453 C Calculate contact energies
2455 wij=cosa-3.0D0*cosb*cosg
2458 c fac3=dsqrt(-ael6i)/r0ij**3
2459 fac3=dsqrt(-ael6i)*r3ij
2460 ees0pij=dsqrt(4.0D0+cosa4+wij*wij-3.0D0*cosbg1*cosbg1)
2461 ees0mij=dsqrt(4.0D0-cosa4+wij*wij-3.0D0*cosbg2*cosbg2)
2463 ees0p(num_conti,i)=0.5D0*fac3*(ees0pij+ees0mij)
2464 ees0m(num_conti,i)=0.5D0*fac3*(ees0pij-ees0mij)
2465 C Diagnostics. Comment out or remove after debugging!
2466 c ees0p(num_conti,i)=0.5D0*fac3*ees0pij
2467 c ees0m(num_conti,i)=0.5D0*fac3*ees0mij
2468 c ees0m(num_conti,i)=0.0D0
2470 c write (iout,*) 'i=',i,' j=',j,' rij=',rij,' r0ij=',r0ij,
2471 c & ' ees0ij=',ees0p(num_conti,i),ees0m(num_conti,i),' fcont=',fcont
2472 facont_hb(num_conti,i)=fcont
2474 C Angular derivatives of the contact function
2475 ees0pij1=fac3/ees0pij
2476 ees0mij1=fac3/ees0mij
2477 fac3p=-3.0D0*fac3*rrmij
2478 ees0pijp=0.5D0*fac3p*(ees0pij+ees0mij)
2479 ees0mijp=0.5D0*fac3p*(ees0pij-ees0mij)
2481 ecosa1= ees0pij1*( 1.0D0+0.5D0*wij)
2482 ecosb1=-1.5D0*ees0pij1*(wij*cosg+cosbg1)
2483 ecosg1=-1.5D0*ees0pij1*(wij*cosb+cosbg1)
2484 ecosa2= ees0mij1*(-1.0D0+0.5D0*wij)
2485 ecosb2=-1.5D0*ees0mij1*(wij*cosg+cosbg2)
2486 ecosg2=-1.5D0*ees0mij1*(wij*cosb-cosbg2)
2487 ecosap=ecosa1+ecosa2
2488 ecosbp=ecosb1+ecosb2
2489 ecosgp=ecosg1+ecosg2
2490 ecosam=ecosa1-ecosa2
2491 ecosbm=ecosb1-ecosb2
2492 ecosgm=ecosg1-ecosg2
2501 fprimcont=fprimcont/rij
2502 cd facont_hb(num_conti,i)=1.0D0
2503 C Following line is for diagnostics.
2506 dcosb(k)=rmij*(dc_norm(k,i)-erij(k)*cosb)
2507 dcosg(k)=rmij*(dc_norm(k,j)-erij(k)*cosg)
2510 gggp(k)=ecosbp*dcosb(k)+ecosgp*dcosg(k)
2511 gggm(k)=ecosbm*dcosb(k)+ecosgm*dcosg(k)
2513 gggp(1)=gggp(1)+ees0pijp*xj
2514 gggp(2)=gggp(2)+ees0pijp*yj
2515 gggp(3)=gggp(3)+ees0pijp*zj
2516 gggm(1)=gggm(1)+ees0mijp*xj
2517 gggm(2)=gggm(2)+ees0mijp*yj
2518 gggm(3)=gggm(3)+ees0mijp*zj
2519 C Derivatives due to the contact function
2520 gacont_hbr(1,num_conti,i)=fprimcont*xj
2521 gacont_hbr(2,num_conti,i)=fprimcont*yj
2522 gacont_hbr(3,num_conti,i)=fprimcont*zj
2524 ghalfp=0.5D0*gggp(k)
2525 ghalfm=0.5D0*gggm(k)
2526 gacontp_hb1(k,num_conti,i)=ghalfp
2527 & +(ecosap*(dc_norm(k,j)-cosa*dc_norm(k,i))
2528 & + ecosbp*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
2529 gacontp_hb2(k,num_conti,i)=ghalfp
2530 & +(ecosap*(dc_norm(k,i)-cosa*dc_norm(k,j))
2531 & + ecosgp*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
2532 gacontp_hb3(k,num_conti,i)=gggp(k)
2533 gacontm_hb1(k,num_conti,i)=ghalfm
2534 & +(ecosam*(dc_norm(k,j)-cosa*dc_norm(k,i))
2535 & + ecosbm*(erij(k)-cosb*dc_norm(k,i)))*vbld_inv(i+1)
2536 gacontm_hb2(k,num_conti,i)=ghalfm
2537 & +(ecosam*(dc_norm(k,i)-cosa*dc_norm(k,j))
2538 & + ecosgm*(erij(k)-cosg*dc_norm(k,j)))*vbld_inv(j+1)
2539 gacontm_hb3(k,num_conti,i)=gggm(k)
2542 C Diagnostics. Comment out or remove after debugging!
2544 cdiag gacontp_hb1(k,num_conti,i)=0.0D0
2545 cdiag gacontp_hb2(k,num_conti,i)=0.0D0
2546 cdiag gacontp_hb3(k,num_conti,i)=0.0D0
2547 cdiag gacontm_hb1(k,num_conti,i)=0.0D0
2548 cdiag gacontm_hb2(k,num_conti,i)=0.0D0
2549 cdiag gacontm_hb3(k,num_conti,i)=0.0D0
2552 endif ! num_conti.le.maxconts
2557 num_cont_hb(i)=num_conti
2561 cd write (iout,'(i3,3f10.5,5x,3f10.5)')
2562 cd & i,(gel_loc(k,i),k=1,3),gel_loc_loc(i)
2564 c 12/7/99 Adam eello_turn3 will be considered as a separate energy term
2565 ccc eel_loc=eel_loc+eello_turn3
2568 C-----------------------------------------------------------------------------
2569 subroutine eturn34(i,j,eello_turn3,eello_turn4)
2570 C Third- and fourth-order contributions from turns
2571 implicit real*8 (a-h,o-z)
2572 include 'DIMENSIONS'
2573 include 'DIMENSIONS.ZSCOPT'
2574 include 'COMMON.IOUNITS'
2575 include 'COMMON.GEO'
2576 include 'COMMON.VAR'
2577 include 'COMMON.LOCAL'
2578 include 'COMMON.CHAIN'
2579 include 'COMMON.DERIV'
2580 include 'COMMON.INTERACT'
2581 include 'COMMON.CONTACTS'
2582 include 'COMMON.TORSION'
2583 include 'COMMON.VECTORS'
2584 include 'COMMON.FFIELD'
2586 double precision auxmat(2,2),auxmat1(2,2),auxmat2(2,2),pizda(2,2),
2587 & e1t(2,2),e2t(2,2),e3t(2,2),e1tder(2,2),e2tder(2,2),e3tder(2,2),
2588 & e1a(2,2),ae3(2,2),ae3e2(2,2),auxvec(2),auxvec1(2)
2589 double precision agg(3,4),aggi(3,4),aggi1(3,4),
2590 & aggj(3,4),aggj1(3,4),a_temp(2,2)
2591 common /locel/ a_temp,agg,aggi,aggi1,aggj,aggj1,j1,j2
2593 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2595 C Third-order contributions
2602 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2603 cd call checkint_turn3(i,a_temp,eello_turn3_num)
2604 call matmat2(EUg(1,1,i+1),EUg(1,1,i+2),auxmat(1,1))
2605 call transpose2(auxmat(1,1),auxmat1(1,1))
2606 call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
2607 eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
2608 cd write (2,*) 'i,',i,' j',j,'eello_turn3',
2609 cd & 0.5d0*(pizda(1,1)+pizda(2,2)),
2610 cd & ' eello_turn3_num',4*eello_turn3_num
2612 C Derivatives in gamma(i)
2613 call matmat2(EUgder(1,1,i+1),EUg(1,1,i+2),auxmat2(1,1))
2614 call transpose2(auxmat2(1,1),pizda(1,1))
2615 call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
2616 gel_loc_turn3(i)=gel_loc_turn3(i)+0.5d0*(pizda(1,1)+pizda(2,2))
2617 C Derivatives in gamma(i+1)
2618 call matmat2(EUg(1,1,i+1),EUgder(1,1,i+2),auxmat2(1,1))
2619 call transpose2(auxmat2(1,1),pizda(1,1))
2620 call matmat2(a_temp(1,1),pizda(1,1),pizda(1,1))
2621 gel_loc_turn3(i+1)=gel_loc_turn3(i+1)
2622 & +0.5d0*(pizda(1,1)+pizda(2,2))
2623 C Cartesian derivatives
2625 a_temp(1,1)=aggi(l,1)
2626 a_temp(1,2)=aggi(l,2)
2627 a_temp(2,1)=aggi(l,3)
2628 a_temp(2,2)=aggi(l,4)
2629 call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
2630 gcorr3_turn(l,i)=gcorr3_turn(l,i)
2631 & +0.5d0*(pizda(1,1)+pizda(2,2))
2632 a_temp(1,1)=aggi1(l,1)
2633 a_temp(1,2)=aggi1(l,2)
2634 a_temp(2,1)=aggi1(l,3)
2635 a_temp(2,2)=aggi1(l,4)
2636 call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
2637 gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1)
2638 & +0.5d0*(pizda(1,1)+pizda(2,2))
2639 a_temp(1,1)=aggj(l,1)
2640 a_temp(1,2)=aggj(l,2)
2641 a_temp(2,1)=aggj(l,3)
2642 a_temp(2,2)=aggj(l,4)
2643 call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
2644 gcorr3_turn(l,j)=gcorr3_turn(l,j)
2645 & +0.5d0*(pizda(1,1)+pizda(2,2))
2646 a_temp(1,1)=aggj1(l,1)
2647 a_temp(1,2)=aggj1(l,2)
2648 a_temp(2,1)=aggj1(l,3)
2649 a_temp(2,2)=aggj1(l,4)
2650 call matmat2(a_temp(1,1),auxmat1(1,1),pizda(1,1))
2651 gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
2652 & +0.5d0*(pizda(1,1)+pizda(2,2))
2655 else if (j.eq.i+3) then
2656 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2658 C Fourth-order contributions
2666 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2667 cd call checkint_turn4(i,a_temp,eello_turn4_num)
2668 iti1=itortyp(itype(i+1))
2669 iti2=itortyp(itype(i+2))
2670 iti3=itortyp(itype(i+3))
2671 call transpose2(EUg(1,1,i+1),e1t(1,1))
2672 call transpose2(Eug(1,1,i+2),e2t(1,1))
2673 call transpose2(Eug(1,1,i+3),e3t(1,1))
2674 call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
2675 call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
2676 s1=scalar2(b1(1,iti2),auxvec(1))
2677 call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
2678 call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
2679 s2=scalar2(b1(1,iti1),auxvec(1))
2680 call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
2681 call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
2682 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2683 eello_turn4=eello_turn4-(s1+s2+s3)
2684 cd write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
2685 cd & ' eello_turn4_num',8*eello_turn4_num
2686 C Derivatives in gamma(i)
2688 call transpose2(EUgder(1,1,i+1),e1tder(1,1))
2689 call matmat2(e1tder(1,1),a_temp(1,1),auxmat(1,1))
2690 call matvec2(auxmat(1,1),Ub2(1,i+3),auxvec(1))
2691 s1=scalar2(b1(1,iti2),auxvec(1))
2692 call matmat2(ae3e2(1,1),e1tder(1,1),pizda(1,1))
2693 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2694 gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
2695 C Derivatives in gamma(i+1)
2696 call transpose2(EUgder(1,1,i+2),e2tder(1,1))
2697 call matvec2(ae3(1,1),Ub2der(1,i+2),auxvec(1))
2698 s2=scalar2(b1(1,iti1),auxvec(1))
2699 call matmat2(ae3(1,1),e2tder(1,1),auxmat(1,1))
2700 call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
2701 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2702 gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
2703 C Derivatives in gamma(i+2)
2704 call transpose2(EUgder(1,1,i+3),e3tder(1,1))
2705 call matvec2(e1a(1,1),Ub2der(1,i+3),auxvec(1))
2706 s1=scalar2(b1(1,iti2),auxvec(1))
2707 call matmat2(a_temp(1,1),e3tder(1,1),auxmat(1,1))
2708 call matvec2(auxmat(1,1),Ub2(1,i+2),auxvec(1))
2709 s2=scalar2(b1(1,iti1),auxvec(1))
2710 call matmat2(auxmat(1,1),e2t(1,1),auxmat(1,1))
2711 call matmat2(auxmat(1,1),e1t(1,1),pizda(1,1))
2712 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2713 gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
2714 C Cartesian derivatives
2715 C Derivatives of this turn contributions in DC(i+2)
2716 if (j.lt.nres-1) then
2718 a_temp(1,1)=agg(l,1)
2719 a_temp(1,2)=agg(l,2)
2720 a_temp(2,1)=agg(l,3)
2721 a_temp(2,2)=agg(l,4)
2722 call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
2723 call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
2724 s1=scalar2(b1(1,iti2),auxvec(1))
2725 call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
2726 call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
2727 s2=scalar2(b1(1,iti1),auxvec(1))
2728 call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
2729 call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
2730 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2732 gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
2735 C Remaining derivatives of this turn contribution
2737 a_temp(1,1)=aggi(l,1)
2738 a_temp(1,2)=aggi(l,2)
2739 a_temp(2,1)=aggi(l,3)
2740 a_temp(2,2)=aggi(l,4)
2741 call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
2742 call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
2743 s1=scalar2(b1(1,iti2),auxvec(1))
2744 call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
2745 call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
2746 s2=scalar2(b1(1,iti1),auxvec(1))
2747 call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
2748 call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
2749 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2750 gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
2751 a_temp(1,1)=aggi1(l,1)
2752 a_temp(1,2)=aggi1(l,2)
2753 a_temp(2,1)=aggi1(l,3)
2754 a_temp(2,2)=aggi1(l,4)
2755 call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
2756 call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
2757 s1=scalar2(b1(1,iti2),auxvec(1))
2758 call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
2759 call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
2760 s2=scalar2(b1(1,iti1),auxvec(1))
2761 call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
2762 call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
2763 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2764 gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
2765 a_temp(1,1)=aggj(l,1)
2766 a_temp(1,2)=aggj(l,2)
2767 a_temp(2,1)=aggj(l,3)
2768 a_temp(2,2)=aggj(l,4)
2769 call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
2770 call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
2771 s1=scalar2(b1(1,iti2),auxvec(1))
2772 call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
2773 call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
2774 s2=scalar2(b1(1,iti1),auxvec(1))
2775 call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
2776 call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
2777 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2778 gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
2779 a_temp(1,1)=aggj1(l,1)
2780 a_temp(1,2)=aggj1(l,2)
2781 a_temp(2,1)=aggj1(l,3)
2782 a_temp(2,2)=aggj1(l,4)
2783 call matmat2(e1t(1,1),a_temp(1,1),e1a(1,1))
2784 call matvec2(e1a(1,1),Ub2(1,i+3),auxvec(1))
2785 s1=scalar2(b1(1,iti2),auxvec(1))
2786 call matmat2(a_temp(1,1),e3t(1,1),ae3(1,1))
2787 call matvec2(ae3(1,1),Ub2(1,i+2),auxvec(1))
2788 s2=scalar2(b1(1,iti1),auxvec(1))
2789 call matmat2(ae3(1,1),e2t(1,1),ae3e2(1,1))
2790 call matmat2(ae3e2(1,1),e1t(1,1),pizda(1,1))
2791 s3=0.5d0*(pizda(1,1)+pizda(2,2))
2792 gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
2798 C-----------------------------------------------------------------------------
2799 subroutine vecpr(u,v,w)
2800 implicit real*8(a-h,o-z)
2801 dimension u(3),v(3),w(3)
2802 w(1)=u(2)*v(3)-u(3)*v(2)
2803 w(2)=-u(1)*v(3)+u(3)*v(1)
2804 w(3)=u(1)*v(2)-u(2)*v(1)
2807 C-----------------------------------------------------------------------------
2808 subroutine unormderiv(u,ugrad,unorm,ungrad)
2809 C This subroutine computes the derivatives of a normalized vector u, given
2810 C the derivatives computed without normalization conditions, ugrad. Returns
2813 double precision u(3),ugrad(3,3),unorm,ungrad(3,3)
2814 double precision vec(3)
2815 double precision scalar
2817 c write (2,*) 'ugrad',ugrad
2820 vec(i)=scalar(ugrad(1,i),u(1))
2822 c write (2,*) 'vec',vec
2825 ungrad(j,i)=(ugrad(j,i)-u(j)*vec(i))*unorm
2828 c write (2,*) 'ungrad',ungrad
2831 C-----------------------------------------------------------------------------
2832 subroutine escp(evdw2,evdw2_14)
2834 C This subroutine calculates the excluded-volume interaction energy between
2835 C peptide-group centers and side chains and its gradient in virtual-bond and
2836 C side-chain vectors.
2838 implicit real*8 (a-h,o-z)
2839 include 'DIMENSIONS'
2840 include 'DIMENSIONS.ZSCOPT'
2841 include 'COMMON.GEO'
2842 include 'COMMON.VAR'
2843 include 'COMMON.LOCAL'
2844 include 'COMMON.CHAIN'
2845 include 'COMMON.DERIV'
2846 include 'COMMON.INTERACT'
2847 include 'COMMON.FFIELD'
2848 include 'COMMON.IOUNITS'
2852 cd print '(a)','Enter ESCP'
2853 c write (iout,*) 'iatscp_s=',iatscp_s,' iatscp_e=',iatscp_e,
2854 c & ' scal14',scal14
2855 do i=iatscp_s,iatscp_e
2857 c write (iout,*) "i",i," iteli",iteli," nscp_gr",nscp_gr(i),
2858 c & " iscp",(iscpstart(i,j),iscpend(i,j),j=1,nscp_gr(i))
2859 if (iteli.eq.0) goto 1225
2860 xi=0.5D0*(c(1,i)+c(1,i+1))
2861 yi=0.5D0*(c(2,i)+c(2,i+1))
2862 zi=0.5D0*(c(3,i)+c(3,i+1))
2864 do iint=1,nscp_gr(i)
2866 do j=iscpstart(i,iint),iscpend(i,iint)
2868 C Uncomment following three lines for SC-p interactions
2872 C Uncomment following three lines for Ca-p interactions
2876 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
2878 e1=fac*fac*aad(itypj,iteli)
2879 e2=fac*bad(itypj,iteli)
2880 if (iabs(j-i) .le. 2) then
2883 evdw2_14=evdw2_14+e1+e2
2886 c write (iout,*) i,j,evdwij
2890 C Calculate contributions to the gradient in the virtual-bond and SC vectors.
2892 fac=-(evdwij+e1)*rrij
2897 cd write (iout,*) 'j<i'
2898 C Uncomment following three lines for SC-p interactions
2900 c gradx_scp(k,j)=gradx_scp(k,j)+ggg(k)
2903 cd write (iout,*) 'j>i'
2906 C Uncomment following line for SC-p interactions
2907 c gradx_scp(k,j)=gradx_scp(k,j)-ggg(k)
2911 gvdwc_scp(k,i)=gvdwc_scp(k,i)-0.5D0*ggg(k)
2915 cd write (iout,*) 'i=',i,' j=',j,' kstart=',kstart,' kend=',kend
2916 cd write (iout,*) ggg(1),ggg(2),ggg(3)
2919 gvdwc_scp(l,k)=gvdwc_scp(l,k)-ggg(l)
2929 gvdwc_scp(j,i)=expon*gvdwc_scp(j,i)
2930 gradx_scp(j,i)=expon*gradx_scp(j,i)
2933 C******************************************************************************
2937 C To save time the factor EXPON has been extracted from ALL components
2938 C of GVDWC and GRADX. Remember to multiply them by this factor before further
2941 C******************************************************************************
2944 C--------------------------------------------------------------------------
2945 subroutine edis(ehpb)
2947 C Evaluate bridge-strain energy and its gradient in virtual-bond and SC vectors.
2949 implicit real*8 (a-h,o-z)
2950 include 'DIMENSIONS'
2951 include 'DIMENSIONS.FREE'
2952 include 'COMMON.SBRIDGE'
2953 include 'COMMON.CHAIN'
2954 include 'COMMON.DERIV'
2955 include 'COMMON.VAR'
2956 include 'COMMON.INTERACT'
2957 include 'COMMON.IOUNITS'
2958 include 'COMMON.CONTROL'
2961 cd write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
2962 cd write(iout,*)'link_start=',link_start,' link_end=',link_end
2963 if (link_end.eq.0) return
2964 do i=link_start,link_end
2965 C If ihpb(i) and jhpb(i) > NRES, this is a SC-SC distance, otherwise a
2966 C CA-CA distance used in regularization of structure.
2969 C iii and jjj point to the residues for which the distance is assigned.
2970 if (ii.gt.nres) then
2977 c write (iout,*) "i",i," ii",ii," iii",iii," jj",jj," jjj",jjj,
2978 c & dhpb(i),dhpb1(i),forcon(i)
2979 C 24/11/03 AL: SS bridges handled separately because of introducing a specific
2980 C distance and angle dependent SS bond potential.
2981 if (.not.dyn_ss .and. i.le.nss) then
2982 C 15/02/13 CC dynamic SSbond - additional check
2983 if (ii.gt.nres .and. itype(iii).eq.1 .and. itype(jjj).eq.1) then
2984 call ssbond_ene(iii,jjj,eij)
2987 cd write (iout,*) "eij",eij
2988 else if (ii.gt.nres .and. jj.gt.nres) then
2989 c Restraints from contact prediction
2991 if (constr_dist.eq.11) then
2992 ehpb=ehpb+fordepth(i)**4.0d0
2993 & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
2994 fac=fordepth(i)**4.0d0
2995 & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
2997 if (dhpb1(i).gt.0.0d0) then
2998 ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
2999 fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
3000 c write (iout,*) "beta nmr",
3001 c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
3005 C Get the force constant corresponding to this distance.
3007 C Calculate the contribution to energy.
3008 ehpb=ehpb+waga*rdis*rdis
3009 c write (iout,*) "beta reg",dd,waga*rdis*rdis
3011 C Evaluate gradient.
3014 endif !end dhpb1(i).gt.0
3015 endif !end const_dist=11
3017 ggg(j)=fac*(c(j,jj)-c(j,ii))
3020 ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
3021 ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
3024 ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
3025 ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
3028 C Calculate the distance between the two points and its difference from the
3031 C write(iout,*) "after",dd
3032 if (constr_dist.eq.11) then
3033 ehpb=ehpb+fordepth(i)**4.0d0
3034 & *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
3035 fac=fordepth(i)**4.0d0
3036 & *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
3037 C ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i))
3038 C fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd
3039 C print *,ehpb,"tu?"
3040 C write(iout,*) ehpb,"btu?",
3041 C & dd,dhpb(i),dhpb1(i),fordepth(i),forcon(i)
3042 C write (iout,'(a6,2i5,3f8.3)') "edisl",ii,jj,
3043 C & ehpb,fordepth(i),dd
3045 if (dhpb1(i).gt.0.0d0) then
3046 ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
3047 fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
3048 c write (iout,*) "alph nmr",
3049 c & dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
3052 C Get the force constant corresponding to this distance.
3054 C Calculate the contribution to energy.
3055 ehpb=ehpb+waga*rdis*rdis
3056 c write (iout,*) "alpha reg",dd,waga*rdis*rdis
3058 C Evaluate gradient.
3063 cd print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
3064 cd & ' waga=',waga,' fac=',fac
3066 ggg(j)=fac*(c(j,jj)-c(j,ii))
3068 cd print '(i3,3(1pe14.5))',i,(ggg(j),j=1,3)
3069 C If this is a SC-SC distance, we need to calculate the contributions to the
3070 C Cartesian gradient in the SC vectors (ghpbx).
3073 ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
3074 ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
3078 ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
3079 ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
3083 if (constr_dist.ne.11) ehpb=0.5D0*ehpb
3086 C--------------------------------------------------------------------------
3087 subroutine ssbond_ene(i,j,eij)
3089 C Calculate the distance and angle dependent SS-bond potential energy
3090 C using a free-energy function derived based on RHF/6-31G** ab initio
3091 C calculations of diethyl disulfide.
3093 C A. Liwo and U. Kozlowska, 11/24/03
3095 implicit real*8 (a-h,o-z)
3096 include 'DIMENSIONS'
3097 include 'DIMENSIONS.ZSCOPT'
3098 include 'COMMON.SBRIDGE'
3099 include 'COMMON.CHAIN'
3100 include 'COMMON.DERIV'
3101 include 'COMMON.LOCAL'
3102 include 'COMMON.INTERACT'
3103 include 'COMMON.VAR'
3104 include 'COMMON.IOUNITS'
3105 double precision erij(3),dcosom1(3),dcosom2(3),gg(3)
3110 dxi=dc_norm(1,nres+i)
3111 dyi=dc_norm(2,nres+i)
3112 dzi=dc_norm(3,nres+i)
3113 dsci_inv=dsc_inv(itypi)
3115 dscj_inv=dsc_inv(itypj)
3119 dxj=dc_norm(1,nres+j)
3120 dyj=dc_norm(2,nres+j)
3121 dzj=dc_norm(3,nres+j)
3122 rrij=1.0D0/(xj*xj+yj*yj+zj*zj)
3127 om1=dxi*erij(1)+dyi*erij(2)+dzi*erij(3)
3128 om2=dxj*erij(1)+dyj*erij(2)+dzj*erij(3)
3129 om12=dxi*dxj+dyi*dyj+dzi*dzj
3131 dcosom1(k)=rij*(dc_norm(k,nres+i)-om1*erij(k))
3132 dcosom2(k)=rij*(dc_norm(k,nres+j)-om2*erij(k))
3138 deltat12=om2-om1+2.0d0
3140 eij=akcm*deltad*deltad+akth*(deltat1*deltat1+deltat2*deltat2)
3141 & +akct*deltad*deltat12+ebr
3142 c & +akct*deltad*deltat12
3143 & +v1ss*cosphi+v2ss*cosphi*cosphi+v3ss*cosphi*cosphi*cosphi
3144 write(iout,*) i,j,"rij",rij,"d0cm",d0cm," akcm",akcm," akth",akth,
3145 & " akct",akct," deltad",deltad," deltat",deltat1,deltat2,
3146 & " deltat12",deltat12," eij",eij,"ebr",ebr
3147 ed=2*akcm*deltad+akct*deltat12
3149 pom2=v1ss+2*v2ss*cosphi+3*v3ss*cosphi*cosphi
3150 eom1=-2*akth*deltat1-pom1-om2*pom2
3151 eom2= 2*akth*deltat2+pom1-om1*pom2
3154 gg(k)=ed*erij(k)+eom1*dcosom1(k)+eom2*dcosom2(k)
3157 ghpbx(k,i)=ghpbx(k,i)-gg(k)
3158 & +(eom12*dc_norm(k,nres+j)+eom1*erij(k))*dsci_inv
3159 ghpbx(k,j)=ghpbx(k,j)+gg(k)
3160 & +(eom12*dc_norm(k,nres+i)+eom2*erij(k))*dscj_inv
3163 C Calculate the components of the gradient in DC and X
3167 ghpbc(l,k)=ghpbc(l,k)+gg(l)
3172 C--------------------------------------------------------------------------
3173 c MODELLER restraint function
3174 subroutine e_modeller(ehomology_constr)
3175 implicit real*8 (a-h,o-z)
3176 include 'DIMENSIONS'
3177 include 'DIMENSIONS.ZSCOPT'
3178 include 'DIMENSIONS.FREE'
3179 integer nnn, i, j, k, ki, irec, l
3180 integer katy, odleglosci, test7
3181 real*8 odleg, odleg2, odleg3, kat, kat2, kat3, gdih(max_template)
3182 real*8 distance(max_template),distancek(max_template),
3183 & min_odl,godl(max_template),dih_diff(max_template)
3186 c FP - 30/10/2014 Temporary specifications for homology restraints
3188 double precision utheta_i,gutheta_i,sum_gtheta,sum_sgtheta,
3190 double precision, dimension (maxres) :: guscdiff,usc_diff
3191 double precision, dimension (max_template) ::
3192 & gtheta,dscdiff,uscdiffk,guscdiff2,guscdiff3,
3195 include 'COMMON.SBRIDGE'
3196 include 'COMMON.CHAIN'
3197 include 'COMMON.GEO'
3198 include 'COMMON.DERIV'
3199 include 'COMMON.LOCAL'
3200 include 'COMMON.INTERACT'
3201 include 'COMMON.VAR'
3202 include 'COMMON.IOUNITS'
3203 include 'COMMON.CONTROL'
3204 include 'COMMON.HOMRESTR'
3206 include 'COMMON.SETUP'
3207 include 'COMMON.NAMES'
3210 distancek(i)=9999999.9
3215 c Pseudo-energy and gradient from homology restraints (MODELLER-like
3217 C AL 5/2/14 - Introduce list of restraints
3218 c write(iout,*) "waga_theta",waga_theta,"waga_d",waga_d
3220 write(iout,*) "------- dist restrs start -------"
3222 do ii = link_start_homo,link_end_homo
3226 c write (iout,*) "dij(",i,j,") =",dij
3228 do k=1,constr_homology
3229 if(.not.l_homo(k,ii)) then
3233 distance(k)=odl(k,ii)-dij
3234 c write (iout,*) "distance(",k,") =",distance(k)
3236 c For Gaussian-type Urestr
3238 distancek(k)=0.5d0*distance(k)**2*sigma_odl(k,ii) ! waga_dist rmvd from Gaussian argument
3239 c write (iout,*) "sigma_odl(",k,ii,") =",sigma_odl(k,ii)
3240 c write (iout,*) "distancek(",k,") =",distancek(k)
3241 c distancek(k)=0.5d0*waga_dist*distance(k)**2*sigma_odl(k,ii)
3243 c For Lorentzian-type Urestr
3245 if (waga_dist.lt.0.0d0) then
3246 sigma_odlir(k,ii)=dsqrt(1/sigma_odl(k,ii))
3247 distancek(k)=distance(k)**2/(sigma_odlir(k,ii)*
3248 & (distance(k)**2+sigma_odlir(k,ii)**2))
3252 c min_odl=minval(distancek)
3253 do kk=1,constr_homology
3254 if(l_homo(kk,ii)) then
3255 min_odl=distancek(kk)
3259 do kk=1,constr_homology
3260 if(l_homo(kk,ii) .and. distancek(kk).lt.min_odl)
3261 & min_odl=distancek(kk)
3263 c write (iout,* )"min_odl",min_odl
3265 write (iout,*) "ij dij",i,j,dij
3266 write (iout,*) "distance",(distance(k),k=1,constr_homology)
3267 write (iout,*) "distancek",(distancek(k),k=1,constr_homology)
3268 write (iout,* )"min_odl",min_odl
3273 if (waga_dist.ge.0.0d0) then
3279 do k=1,constr_homology
3280 c Nie wiem po co to liczycie jeszcze raz!
3281 c odleg3=-waga_dist(iset)*((distance(i,j,k)**2)/
3282 c & (2*(sigma_odl(i,j,k))**2))
3283 if(.not.l_homo(k,ii)) cycle
3284 if (waga_dist.ge.0.0d0) then
3286 c For Gaussian-type Urestr
3288 godl(k)=dexp(-distancek(k)+min_odl)
3289 odleg2=odleg2+godl(k)
3291 c For Lorentzian-type Urestr
3294 odleg2=odleg2+distancek(k)
3297 ccc write(iout,779) i,j,k, "odleg2=",odleg2, "odleg3=", odleg3,
3298 ccc & "dEXP(odleg3)=", dEXP(odleg3),"distance(i,j,k)^2=",
3299 ccc & distance(i,j,k)**2, "dist(i+1,j+1)=", dist(i+1,j+1),
3300 ccc & "sigma_odl(i,j,k)=", sigma_odl(i,j,k)
3303 c write (iout,*) "godl",(godl(k),k=1,constr_homology) ! exponents
3304 c write (iout,*) "ii i j",ii,i,j," odleg2",odleg2 ! sum of exps
3306 write (iout,*) "godl",(godl(k),k=1,constr_homology) ! exponents
3307 write (iout,*) "ii i j",ii,i,j," odleg2",odleg2 ! sum of exps
3309 if (waga_dist.ge.0.0d0) then
3311 c For Gaussian-type Urestr
3313 odleg=odleg-dLOG(odleg2/constr_homology)+min_odl
3315 c For Lorentzian-type Urestr
3318 odleg=odleg+odleg2/constr_homology
3322 c write (iout,*) "odleg",odleg ! sum of -ln-s
3325 c For Gaussian-type Urestr
3327 if (waga_dist.ge.0.0d0) sum_godl=odleg2
3329 do k=1,constr_homology
3330 c godl=dexp(((-(distance(i,j,k)**2)/(2*(sigma_odl(i,j,k))**2))
3331 c & *waga_dist)+min_odl
3332 c sgodl=-godl(k)*distance(k)*sigma_odl(k,ii)*waga_dist
3334 if(.not.l_homo(k,ii)) cycle
3335 if (waga_dist.ge.0.0d0) then
3336 c For Gaussian-type Urestr
3338 sgodl=-godl(k)*distance(k)*sigma_odl(k,ii) ! waga_dist rmvd
3340 c For Lorentzian-type Urestr
3343 sgodl=-2*sigma_odlir(k,ii)*(distance(k)/(distance(k)**2+
3344 & sigma_odlir(k,ii)**2)**2)
3346 sum_sgodl=sum_sgodl+sgodl
3348 c sgodl2=sgodl2+sgodl
3349 c write(iout,*) i, j, k, distance(i,j,k), "W GRADIENCIE1"
3350 c write(iout,*) "constr_homology=",constr_homology
3351 c write(iout,*) i, j, k, "TEST K"
3353 if (waga_dist.ge.0.0d0) then
3355 c For Gaussian-type Urestr
3357 grad_odl3=waga_homology(iset)*waga_dist
3358 & *sum_sgodl/(sum_godl*dij)
3360 c For Lorentzian-type Urestr
3363 c Original grad expr modified by analogy w Gaussian-type Urestr grad
3364 c grad_odl3=-waga_homology(iset)*waga_dist*sum_sgodl
3365 grad_odl3=-waga_homology(iset)*waga_dist*
3366 & sum_sgodl/(constr_homology*dij)
3369 c grad_odl3=sum_sgodl/(sum_godl*dij)
3372 c write(iout,*) i, j, k, distance(i,j,k), "W GRADIENCIE2"
3373 c write(iout,*) (distance(i,j,k)**2), (2*(sigma_odl(i,j,k))**2),
3374 c & (-(distance(i,j,k)**2)/(2*(sigma_odl(i,j,k))**2))
3376 ccc write(iout,*) godl, sgodl, grad_odl3
3378 c grad_odl=grad_odl+grad_odl3
3381 ggodl=grad_odl3*(c(jik,i)-c(jik,j))
3382 ccc write(iout,*) c(jik,i+1), c(jik,j+1), (c(jik,i+1)-c(jik,j+1))
3383 ccc write(iout,746) "GRAD_ODL_1", i, j, jik, ggodl,
3384 ccc & ghpbc(jik,i+1), ghpbc(jik,j+1)
3385 ghpbc(jik,i)=ghpbc(jik,i)+ggodl
3386 ghpbc(jik,j)=ghpbc(jik,j)-ggodl
3387 ccc write(iout,746) "GRAD_ODL_2", i, j, jik, ggodl,
3388 ccc & ghpbc(jik,i+1), ghpbc(jik,j+1)
3389 c if (i.eq.25.and.j.eq.27) then
3390 c write(iout,*) "jik",jik,"i",i,"j",j
3391 c write(iout,*) "sum_sgodl",sum_sgodl,"sgodl",sgodl
3392 c write(iout,*) "grad_odl3",grad_odl3
3393 c write(iout,*) "c(",jik,i,")",c(jik,i),"c(",jik,j,")",c(jik,j)
3394 c write(iout,*) "ggodl",ggodl
3395 c write(iout,*) "ghpbc(",jik,i,")",
3396 c & ghpbc(jik,i),"ghpbc(",jik,j,")",
3401 ccc write(iout,778)"TEST: odleg2=", odleg2, "DLOG(odleg2)=",
3402 ccc & dLOG(odleg2),"-odleg=", -odleg
3404 enddo ! ii-loop for dist
3406 write(iout,*) "------- dist restrs end -------"
3407 c if (waga_angle.eq.1.0d0 .or. waga_theta.eq.1.0d0 .or.
3408 c & waga_d.eq.1.0d0) call sum_gradient
3410 c Pseudo-energy and gradient from dihedral-angle restraints from
3411 c homology templates
3412 c write (iout,*) "End of distance loop"
3415 c write (iout,*) idihconstr_start_homo,idihconstr_end_homo
3417 write(iout,*) "------- dih restrs start -------"
3418 do i=idihconstr_start_homo,idihconstr_end_homo
3419 write (iout,*) "gloc_init(",i,icg,")",gloc(i,icg)
3422 do i=idihconstr_start_homo,idihconstr_end_homo
3424 c betai=beta(i,i+1,i+2,i+3)
3426 c write (iout,*) "betai =",betai
3427 do k=1,constr_homology
3428 dih_diff(k)=pinorm(dih(k,i)-betai)
3429 c write (iout,*) "dih_diff(",k,") =",dih_diff(k)
3430 c if (dih_diff(i,k).gt.3.14159) dih_diff(i,k)=
3431 c & -(6.28318-dih_diff(i,k))
3432 c if (dih_diff(i,k).lt.-3.14159) dih_diff(i,k)=
3433 c & 6.28318+dih_diff(i,k)
3435 kat3=-0.5d0*dih_diff(k)**2*sigma_dih(k,i) ! waga_angle rmvd from Gaussian argument
3437 kat3=(dcos(dih_diff(k))-1)*sigma_dih(k,i)
3439 c kat3=-0.5d0*waga_angle*dih_diff(k)**2*sigma_dih(k,i)
3442 c write(iout,*) "kat2=", kat2, "exp(kat3)=", exp(kat3)
3445 c write (iout,*) "gdih",(gdih(k),k=1,constr_homology) ! exps
3446 c write (iout,*) "i",i," betai",betai," kat2",kat2 ! sum of exps
3448 write (iout,*) "i",i," betai",betai," kat2",kat2
3449 write (iout,*) "gdih",(gdih(k),k=1,constr_homology)
3451 if (kat2.le.1.0d-14) cycle
3452 kat=kat-dLOG(kat2/constr_homology)
3453 c write (iout,*) "kat",kat ! sum of -ln-s
3455 ccc write(iout,778)"TEST: kat2=", kat2, "DLOG(kat2)=",
3456 ccc & dLOG(kat2), "-kat=", -kat
3459 c ----------------------------------------------------------------------
3461 c ----------------------------------------------------------------------
3465 do k=1,constr_homology
3467 sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i) ! waga_angle rmvd
3469 sgdih=-gdih(k)*dsin(dih_diff(k))*sigma_dih(k,i)
3471 c sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i)*waga_angle
3472 sum_sgdih=sum_sgdih+sgdih
3474 c grad_dih3=sum_sgdih/sum_gdih
3475 grad_dih3=waga_homology(iset)*waga_angle*sum_sgdih/sum_gdih
3477 c write(iout,*)i,k,gdih,sgdih,beta(i+1,i+2,i+3,i+4),grad_dih3
3478 ccc write(iout,747) "GRAD_KAT_1", i, nphi, icg, grad_dih3,
3479 ccc & gloc(nphi+i-3,icg)
3480 gloc(i,icg)=gloc(i,icg)+grad_dih3
3482 c write(iout,*) "i",i,"icg",icg,"gloc(",i,icg,")",gloc(i,icg)
3484 ccc write(iout,747) "GRAD_KAT_2", i, nphi, icg, grad_dih3,
3485 ccc & gloc(nphi+i-3,icg)
3487 enddo ! i-loop for dih
3489 write(iout,*) "------- dih restrs end -------"
3492 c Pseudo-energy and gradient for theta angle restraints from
3493 c homology templates
3494 c FP 01/15 - inserted from econstr_local_test.F, loop structure
3498 c For constr_homology reference structures (FP)
3500 c Uconst_back_tot=0.0d0
3503 c Econstr_back legacy
3506 c do i=ithet_start,ithet_end
3509 c do i=loc_start,loc_end
3512 duscdiffx(j,i)=0.0d0
3518 c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
3519 c write (iout,*) "waga_theta",waga_theta
3520 if (waga_theta.gt.0.0d0) then
3522 write (iout,*) "usampl",usampl
3523 write(iout,*) "------- theta restrs start -------"
3524 c do i=ithet_start,ithet_end
3525 c write (iout,*) "gloc_init(",nphi+i,icg,")",gloc(nphi+i,icg)
3528 c write (iout,*) "maxres",maxres,"nres",nres
3530 do i=ithet_start,ithet_end
3533 c ii = ifrag_back(2,i,iset)-ifrag_back(1,i,iset)
3535 c Deviation of theta angles wrt constr_homology ref structures
3537 utheta_i=0.0d0 ! argument of Gaussian for single k
3538 gutheta_i=0.0d0 ! Sum of Gaussians over constr_homology ref structures
3539 c do j=ifrag_back(1,i,iset)+2,ifrag_back(2,i,iset) ! original loop
3540 c over residues in a fragment
3541 c write (iout,*) "theta(",i,")=",theta(i)
3542 do k=1,constr_homology
3544 c dtheta_i=theta(j)-thetaref(j,iref)
3545 c dtheta_i=thetaref(k,i)-theta(i) ! original form without indexing
3546 theta_diff(k)=thetatpl(k,i)-theta(i)
3548 utheta_i=-0.5d0*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta rmvd from Gaussian argument
3549 c utheta_i=-0.5d0*waga_theta*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta?
3550 gtheta(k)=dexp(utheta_i) ! + min_utheta_i?
3551 gutheta_i=gutheta_i+dexp(utheta_i) ! Sum of Gaussians (pk)
3552 c Gradient for single Gaussian restraint in subr Econstr_back
3553 c dutheta(j-2)=dutheta(j-2)+wfrag_back(1,i,iset)*dtheta_i/(ii-1)
3556 c write (iout,*) "gtheta",(gtheta(k),k=1,constr_homology) ! exps
3557 c write (iout,*) "i",i," gutheta_i",gutheta_i ! sum of exps
3561 c Gradient for multiple Gaussian restraint
3562 sum_gtheta=gutheta_i
3564 do k=1,constr_homology
3565 c New generalized expr for multiple Gaussian from Econstr_back
3566 sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i) ! waga_theta rmvd
3568 c sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i)*waga_theta ! right functional form?
3569 sum_sgtheta=sum_sgtheta+sgtheta ! cum variable
3572 c Final value of gradient using same var as in Econstr_back
3573 dutheta(i-2)=sum_sgtheta/sum_gtheta*waga_theta
3574 & *waga_homology(iset)
3575 c dutheta(i)=sum_sgtheta/sum_gtheta
3577 c Uconst_back=Uconst_back+waga_theta*utheta(i) ! waga_theta added as weight
3579 Eval=Eval-dLOG(gutheta_i/constr_homology)
3580 c write (iout,*) "utheta(",i,")=",utheta(i) ! -ln of sum of exps
3581 c write (iout,*) "Uconst_back",Uconst_back ! sum of -ln-s
3582 c Uconst_back=Uconst_back+utheta(i)
3583 enddo ! (i-loop for theta)
3585 write(iout,*) "------- theta restrs end -------"
3589 c Deviation of local SC geometry
3591 c Separation of two i-loops (instructed by AL - 11/3/2014)
3593 c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
3594 c write (iout,*) "waga_d",waga_d
3597 write(iout,*) "------- SC restrs start -------"
3598 write (iout,*) "Initial duscdiff,duscdiffx"
3599 do i=loc_start,loc_end
3600 write (iout,*) i,(duscdiff(jik,i),jik=1,3),
3601 & (duscdiffx(jik,i),jik=1,3)
3604 do i=loc_start,loc_end
3605 usc_diff_i=0.0d0 ! argument of Gaussian for single k
3606 guscdiff(i)=0.0d0 ! Sum of Gaussians over constr_homology ref structures
3607 c do j=ifrag_back(1,i,iset)+1,ifrag_back(2,i,iset)-1 ! Econstr_back legacy
3608 c write(iout,*) "xxtab, yytab, zztab"
3609 c write(iout,'(i5,3f8.2)') i,xxtab(i),yytab(i),zztab(i)
3610 do k=1,constr_homology
3612 dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
3613 c Original sign inverted for calc of gradients (s. Econstr_back)
3614 dyy=-yytpl(k,i)+yytab(i) ! ibid y
3615 dzz=-zztpl(k,i)+zztab(i) ! ibid z
3616 c write(iout,*) "dxx, dyy, dzz"
3617 c write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
3619 usc_diff_i=-0.5d0*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d rmvd from Gaussian argument
3620 c usc_diff(i)=-0.5d0*waga_d*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d?
3621 c uscdiffk(k)=usc_diff(i)
3622 guscdiff2(k)=dexp(usc_diff_i) ! without min_scdiff
3623 guscdiff(i)=guscdiff(i)+dexp(usc_diff_i) !Sum of Gaussians (pk)
3624 c write (iout,'(i5,6f10.5)') j,xxtab(j),yytab(j),zztab(j),
3625 c & xxref(j),yyref(j),zzref(j)
3630 c Generalized expression for multiple Gaussian acc to that for a single
3631 c Gaussian in Econstr_back as instructed by AL (FP - 03/11/2014)
3633 c Original implementation
3634 c sum_guscdiff=guscdiff(i)
3636 c sum_sguscdiff=0.0d0
3637 c do k=1,constr_homology
3638 c sguscdiff=-guscdiff2(k)*dscdiff(k)*sigma_d(k,i)*waga_d !waga_d?
3639 c sguscdiff=-guscdiff3(k)*dscdiff(k)*sigma_d(k,i)*waga_d ! w min_uscdiff
3640 c sum_sguscdiff=sum_sguscdiff+sguscdiff
3643 c Implementation of new expressions for gradient (Jan. 2015)
3645 c grad_uscdiff=sum_sguscdiff/(sum_guscdiff*dtab) !?
3647 do k=1,constr_homology
3649 c New calculation of dxx, dyy, and dzz corrected by AL (07/11), was missing and wrong
3650 c before. Now the drivatives should be correct
3652 dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
3653 c Original sign inverted for calc of gradients (s. Econstr_back)
3654 dyy=-yytpl(k,i)+yytab(i) ! ibid y
3655 dzz=-zztpl(k,i)+zztab(i) ! ibid z
3657 c New implementation
3659 sum_guscdiff=guscdiff2(k)*!(dsqrt(dxx*dxx+dyy*dyy+dzz*dzz))* -> wrong!
3660 & sigma_d(k,i) ! for the grad wrt r'
3661 c sum_sguscdiff=sum_sguscdiff+sum_guscdiff
3664 c New implementation
3665 sum_guscdiff = waga_homology(iset)*waga_d*sum_guscdiff
3667 duscdiff(jik,i-1)=duscdiff(jik,i-1)+
3668 & sum_guscdiff*(dXX_C1tab(jik,i)*dxx+
3669 & dYY_C1tab(jik,i)*dyy+dZZ_C1tab(jik,i)*dzz)/guscdiff(i)
3670 duscdiff(jik,i)=duscdiff(jik,i)+
3671 & sum_guscdiff*(dXX_Ctab(jik,i)*dxx+
3672 & dYY_Ctab(jik,i)*dyy+dZZ_Ctab(jik,i)*dzz)/guscdiff(i)
3673 duscdiffx(jik,i)=duscdiffx(jik,i)+
3674 & sum_guscdiff*(dXX_XYZtab(jik,i)*dxx+
3675 & dYY_XYZtab(jik,i)*dyy+dZZ_XYZtab(jik,i)*dzz)/guscdiff(i)
3678 write(iout,*) "jik",jik,"i",i
3679 write(iout,*) "dxx, dyy, dzz"
3680 write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
3681 write(iout,*) "guscdiff2(",k,")",guscdiff2(k)
3682 c write(iout,*) "sum_sguscdiff",sum_sguscdiff
3683 cc write(iout,*) "dXX_Ctab(",jik,i,")",dXX_Ctab(jik,i)
3684 c write(iout,*) "dYY_Ctab(",jik,i,")",dYY_Ctab(jik,i)
3685 c write(iout,*) "dZZ_Ctab(",jik,i,")",dZZ_Ctab(jik,i)
3686 c write(iout,*) "dXX_C1tab(",jik,i,")",dXX_C1tab(jik,i)
3687 c write(iout,*) "dYY_C1tab(",jik,i,")",dYY_C1tab(jik,i)
3688 c write(iout,*) "dZZ_C1tab(",jik,i,")",dZZ_C1tab(jik,i)
3689 c write(iout,*) "dXX_XYZtab(",jik,i,")",dXX_XYZtab(jik,i)
3690 c write(iout,*) "dYY_XYZtab(",jik,i,")",dYY_XYZtab(jik,i)
3691 c write(iout,*) "dZZ_XYZtab(",jik,i,")",dZZ_XYZtab(jik,i)
3692 c write(iout,*) "duscdiff(",jik,i-1,")",duscdiff(jik,i-1)
3693 c write(iout,*) "duscdiff(",jik,i,")",duscdiff(jik,i)
3694 c write(iout,*) "duscdiffx(",jik,i,")",duscdiffx(jik,i)
3701 c uscdiff(i)=-dLOG(guscdiff(i)/(ii-1)) ! Weighting by (ii-1) required?
3702 c usc_diff(i)=-dLOG(guscdiff(i)/constr_homology) ! + min_uscdiff ?
3704 c write (iout,*) i," uscdiff",uscdiff(i)
3706 c Put together deviations from local geometry
3708 c Uconst_back=Uconst_back+wfrag_back(1,i,iset)*utheta(i)+
3709 c & wfrag_back(3,i,iset)*uscdiff(i)
3710 Erot=Erot-dLOG(guscdiff(i)/constr_homology)
3711 c write (iout,*) "usc_diff(",i,")=",usc_diff(i) ! -ln of sum of exps
3712 c write (iout,*) "Uconst_back",Uconst_back ! cum sum of -ln-s
3713 c Uconst_back=Uconst_back+usc_diff(i)
3715 c Gradient of multiple Gaussian restraint (FP - 04/11/2014 - right?)
3717 c New implment: multiplied by sum_sguscdiff
3720 enddo ! (i-loop for dscdiff)
3725 write(iout,*) "------- SC restrs end -------"
3726 write (iout,*) "------ After SC loop in e_modeller ------"
3727 do i=loc_start,loc_end
3728 write (iout,*) "i",i," gradc",(gradc(j,i,icg),j=1,3)
3729 write (iout,*) "i",i," gradx",(gradx(j,i,icg),j=1,3)
3731 if (waga_theta.eq.1.0d0) then
3732 write (iout,*) "in e_modeller after SC restr end: dutheta"
3733 do i=ithet_start,ithet_end
3734 write (iout,*) i,dutheta(i)
3737 if (waga_d.eq.1.0d0) then
3738 write (iout,*) "e_modeller after SC loop: duscdiff/x"
3740 write (iout,*) i,(duscdiff(j,i),j=1,3)
3741 write (iout,*) i,(duscdiffx(j,i),j=1,3)
3746 c Total energy from homology restraints
3748 write (iout,*) "odleg",odleg," kat",kat
3749 write (iout,*) "odleg",odleg," kat",kat
3750 write (iout,*) "Eval",Eval," Erot",Erot
3751 write (iout,*) "waga_homology(",iset,")",waga_homology(iset)
3752 write (iout,*) "waga_dist ",waga_dist,"waga_angle ",waga_angle
3753 write (iout,*) "waga_theta ",waga_theta,"waga_d ",waga_d
3756 c Addition of energy of theta angle and SC local geom over constr_homologs ref strs
3758 c ehomology_constr=odleg+kat
3760 c For Lorentzian-type Urestr
3763 if (waga_dist.ge.0.0d0) then
3765 c For Gaussian-type Urestr
3767 c ehomology_constr=(waga_dist*odleg+waga_angle*kat+
3768 c & waga_theta*Eval+waga_d*Erot)*waga_homology(iset)
3769 ehomology_constr=waga_dist*odleg+waga_angle*kat+
3770 & waga_theta*Eval+waga_d*Erot
3771 c write (iout,*) "ehomology_constr=",ehomology_constr
3774 c For Lorentzian-type Urestr
3776 c ehomology_constr=(-waga_dist*odleg+waga_angle*kat+
3777 c & waga_theta*Eval+waga_d*Erot)*waga_homology(iset)
3778 ehomology_constr=-waga_dist*odleg+waga_angle*kat+
3779 & waga_theta*Eval+waga_d*Erot
3780 c write (iout,*) "ehomology_constr=",ehomology_constr
3783 write (iout,*) "odleg",waga_dist,odleg," kat",waga_angle,kat,
3784 & "Eval",waga_theta,eval,
3785 & "Erot",waga_d,Erot
3786 write (iout,*) "ehomology_constr",ehomology_constr
3790 748 format(a8,f12.3,a6,f12.3,a7,f12.3)
3791 747 format(a12,i4,i4,i4,f8.3,f8.3)
3792 746 format(a12,i4,i4,i4,f8.3,f8.3,f8.3)
3793 778 format(a7,1X,f10.3,1X,a4,1X,f10.3,1X,a5,1X,f10.3)
3794 779 format(i3,1X,i3,1X,i2,1X,a7,1X,f7.3,1X,a7,1X,f7.3,1X,a13,1X,
3795 & f7.3,1X,a17,1X,f9.3,1X,a10,1X,f8.3,1X,a10,1X,f8.3)
3797 c-----------------------------------------------------------------------
3798 subroutine ebond(estr)
3800 c Evaluate the energy of stretching of the CA-CA and CA-SC virtual bonds
3802 implicit real*8 (a-h,o-z)
3803 include 'DIMENSIONS'
3804 include 'DIMENSIONS.ZSCOPT'
3805 include 'DIMENSIONS.FREE'
3806 include 'COMMON.LOCAL'
3807 include 'COMMON.GEO'
3808 include 'COMMON.INTERACT'
3809 include 'COMMON.DERIV'
3810 include 'COMMON.VAR'
3811 include 'COMMON.CHAIN'
3812 include 'COMMON.IOUNITS'
3813 include 'COMMON.NAMES'
3814 include 'COMMON.FFIELD'
3815 include 'COMMON.CONTROL'
3816 double precision u(3),ud(3)
3817 logical :: lprn=.false.
3820 diff = vbld(i)-vbldp0
3821 c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
3824 gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i)
3829 c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
3836 diff=vbld(i+nres)-vbldsc0(1,iti)
3838 & write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
3839 & AKSC(1,iti),AKSC(1,iti)*diff*diff
3840 estr=estr+0.5d0*AKSC(1,iti)*diff*diff
3842 gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
3846 diff=vbld(i+nres)-vbldsc0(j,iti)
3847 ud(j)=aksc(j,iti)*diff
3848 u(j)=abond0(j,iti)+0.5d0*ud(j)*diff
3862 uprod2=uprod2*u(k)*u(k)
3866 usumsqder=usumsqder+ud(j)*uprod2
3869 & write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti),
3870 & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi)
3871 estr=estr+uprod/usum
3873 gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
3881 C--------------------------------------------------------------------------
3882 subroutine ebend(etheta)
3884 C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
3885 C angles gamma and its derivatives in consecutive thetas and gammas.
3887 implicit real*8 (a-h,o-z)
3888 include 'DIMENSIONS'
3889 include 'DIMENSIONS.ZSCOPT'
3890 include 'COMMON.LOCAL'
3891 include 'COMMON.GEO'
3892 include 'COMMON.INTERACT'
3893 include 'COMMON.DERIV'
3894 include 'COMMON.VAR'
3895 include 'COMMON.CHAIN'
3896 include 'COMMON.IOUNITS'
3897 include 'COMMON.NAMES'
3898 include 'COMMON.FFIELD'
3899 common /calcthet/ term1,term2,termm,diffak,ratak,
3900 & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
3901 & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
3902 double precision y(2),z(2)
3904 time11=dexp(-2*time)
3907 c write (iout,*) "nres",nres
3908 c write (*,'(a,i2)') 'EBEND ICG=',icg
3909 c write (iout,*) ithet_start,ithet_end
3910 do i=ithet_start,ithet_end
3911 C Zero the energy function and its derivative at 0 or pi.
3912 call splinthet(theta(i),0.5d0*delta,ss,ssd)
3914 c if (i.gt.ithet_start .and.
3915 c & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215
3916 c if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then
3924 c if (i.lt.nres .and. itel(i).ne.0) then
3936 call proc_proc(phii,icrc)
3937 if (icrc.eq.1) phii=150.0
3951 call proc_proc(phii1,icrc)
3952 if (icrc.eq.1) phii1=150.0
3964 C Calculate the "mean" value of theta from the part of the distribution
3965 C dependent on the adjacent virtual-bond-valence angles (gamma1 & gamma2).
3966 C In following comments this theta will be referred to as t_c.
3967 thet_pred_mean=0.0d0
3971 thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
3973 c write (iout,*) "thet_pred_mean",thet_pred_mean
3974 dthett=thet_pred_mean*ssd
3975 thet_pred_mean=thet_pred_mean*ss+a0thet(it)
3976 c write (iout,*) "thet_pred_mean",thet_pred_mean
3977 C Derivatives of the "mean" values in gamma1 and gamma2.
3978 dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
3979 dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
3980 if (theta(i).gt.pi-delta) then
3981 call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
3983 call mixder(pi-delta,thet_pred_mean,theta0(it),fprim_tc0)
3984 call theteng(pi,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
3985 call spline1(theta(i),pi-delta,delta,f0,f1,fprim0,ethetai,
3987 call spline2(theta(i),pi-delta,delta,E_tc0,E_tc1,fprim_tc0,
3989 else if (theta(i).lt.delta) then
3990 call theteng(delta,thet_pred_mean,theta0(it),f0,fprim0,E_tc0)
3991 call theteng(0.0d0,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
3992 call spline1(theta(i),delta,-delta,f0,f1,fprim0,ethetai,
3994 call mixder(delta,thet_pred_mean,theta0(it),fprim_tc0)
3995 call spline2(theta(i),delta,-delta,E_tc0,E_tc1,fprim_tc0,
3998 call theteng(theta(i),thet_pred_mean,theta0(it),ethetai,
4001 etheta=etheta+ethetai
4002 c write (iout,'(2i3,3f8.3,f10.5)') i,it,rad2deg*theta(i),
4003 c & rad2deg*phii,rad2deg*phii1,ethetai
4004 if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1
4005 if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2
4006 gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)
4009 C Ufff.... We've done all this!!!
4012 C---------------------------------------------------------------------------
4013 subroutine theteng(thetai,thet_pred_mean,theta0i,ethetai,E_theta,
4015 implicit real*8 (a-h,o-z)
4016 include 'DIMENSIONS'
4017 include 'COMMON.LOCAL'
4018 include 'COMMON.IOUNITS'
4019 common /calcthet/ term1,term2,termm,diffak,ratak,
4020 & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
4021 & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
4022 C Calculate the contributions to both Gaussian lobes.
4023 C 6/6/97 - Deform the Gaussians using the factor of 1/(1+time)
4024 C The "polynomial part" of the "standard deviation" of this part of
4028 sig=sig*thet_pred_mean+polthet(j,it)
4030 C Derivative of the "interior part" of the "standard deviation of the"
4031 C gamma-dependent Gaussian lobe in t_c.
4032 sigtc=3*polthet(3,it)
4034 sigtc=sigtc*thet_pred_mean+j*polthet(j,it)
4037 C Set the parameters of both Gaussian lobes of the distribution.
4038 C "Standard deviation" of the gamma-dependent Gaussian lobe (sigtc)
4039 fac=sig*sig+sigc0(it)
4042 C Following variable (sigsqtc) is -(1/2)d[sigma(t_c)**(-2))]/dt_c
4043 sigsqtc=-4.0D0*sigcsq*sigtc
4044 c print *,i,sig,sigtc,sigsqtc
4045 C Following variable (sigtc) is d[sigma(t_c)]/dt_c
4046 sigtc=-sigtc/(fac*fac)
4047 C Following variable is sigma(t_c)**(-2)
4048 sigcsq=sigcsq*sigcsq
4050 sig0inv=1.0D0/sig0i**2
4051 delthec=thetai-thet_pred_mean
4052 delthe0=thetai-theta0i
4053 term1=-0.5D0*sigcsq*delthec*delthec
4054 term2=-0.5D0*sig0inv*delthe0*delthe0
4055 C Following fuzzy logic is to avoid underflows in dexp and subsequent INFs and
4056 C NaNs in taking the logarithm. We extract the largest exponent which is added
4057 C to the energy (this being the log of the distribution) at the end of energy
4058 C term evaluation for this virtual-bond angle.
4059 if (term1.gt.term2) then
4061 term2=dexp(term2-termm)
4065 term1=dexp(term1-termm)
4068 C The ratio between the gamma-independent and gamma-dependent lobes of
4069 C the distribution is a Gaussian function of thet_pred_mean too.
4070 diffak=gthet(2,it)-thet_pred_mean
4071 ratak=diffak/gthet(3,it)**2
4072 ak=dexp(gthet(1,it)-0.5D0*diffak*ratak)
4073 C Let's differentiate it in thet_pred_mean NOW.
4075 C Now put together the distribution terms to make complete distribution.
4076 termexp=term1+ak*term2
4077 termpre=sigc+ak*sig0i
4078 C Contribution of the bending energy from this theta is just the -log of
4079 C the sum of the contributions from the two lobes and the pre-exponential
4080 C factor. Simple enough, isn't it?
4081 ethetai=(-dlog(termexp)-termm+dlog(termpre))
4082 C NOW the derivatives!!!
4083 C 6/6/97 Take into account the deformation.
4084 E_theta=(delthec*sigcsq*term1
4085 & +ak*delthe0*sig0inv*term2)/termexp
4086 E_tc=((sigtc+aktc*sig0i)/termpre
4087 & -((delthec*sigcsq+delthec*delthec*sigsqtc)*term1+
4088 & aktc*term2)/termexp)
4091 c-----------------------------------------------------------------------------
4092 subroutine mixder(thetai,thet_pred_mean,theta0i,E_tc_t)
4093 implicit real*8 (a-h,o-z)
4094 include 'DIMENSIONS'
4095 include 'COMMON.LOCAL'
4096 include 'COMMON.IOUNITS'
4097 common /calcthet/ term1,term2,termm,diffak,ratak,
4098 & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
4099 & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
4100 delthec=thetai-thet_pred_mean
4101 delthe0=thetai-theta0i
4102 C "Thank you" to MAPLE (probably spared one day of hand-differentiation).
4103 t3 = thetai-thet_pred_mean
4107 t14 = t12+t6*sigsqtc
4109 t21 = thetai-theta0i
4115 E_tc_t = -((sigcsq+2.D0*t3*sigsqtc)*t9-t14*sigcsq*t3*t16*t9
4116 & -aktc*sig0inv*t27)/t32+(t14*t9+aktc*t26)/t40
4117 & *(-t12*t9-ak*sig0inv*t27)
4121 C--------------------------------------------------------------------------
4122 subroutine ebend(etheta)
4124 C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
4125 C angles gamma and its derivatives in consecutive thetas and gammas.
4126 C ab initio-derived potentials from
4127 c Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
4129 implicit real*8 (a-h,o-z)
4130 include 'DIMENSIONS'
4131 include 'DIMENSIONS.ZSCOPT'
4132 include 'DIMENSIONS.FREE'
4133 include 'COMMON.LOCAL'
4134 include 'COMMON.GEO'
4135 include 'COMMON.INTERACT'
4136 include 'COMMON.DERIV'
4137 include 'COMMON.VAR'
4138 include 'COMMON.CHAIN'
4139 include 'COMMON.IOUNITS'
4140 include 'COMMON.NAMES'
4141 include 'COMMON.FFIELD'
4142 include 'COMMON.CONTROL'
4143 double precision coskt(mmaxtheterm),sinkt(mmaxtheterm),
4144 & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle),
4145 & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble),
4146 & sinph1ph2(maxdouble,maxdouble)
4147 logical lprn /.false./, lprn1 /.false./
4149 c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
4150 do i=ithet_start,ithet_end
4151 if ((itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
4152 & (itype(i).eq.ntyp1)) cycle
4156 theti2=0.5d0*theta(i)
4157 ityp2=ithetyp(itype(i-1))
4159 coskt(k)=dcos(k*theti2)
4160 sinkt(k)=dsin(k*theti2)
4162 if (i.gt.3 .and. itype(max0(i-3,1)).ne.ntyp1) then
4165 if (phii.ne.phii) phii=150.0
4169 ityp1=ithetyp(itype(i-2))
4171 cosph1(k)=dcos(k*phii)
4172 sinph1(k)=dsin(k*phii)
4176 ityp1=ithetyp(itype(i-2))
4182 if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
4185 if (phii1.ne.phii1) phii1=150.0
4190 ityp3=ithetyp(itype(i))
4192 cosph2(k)=dcos(k*phii1)
4193 sinph2(k)=dsin(k*phii1)
4198 ityp3=ithetyp(itype(i))
4204 c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
4205 c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
4207 ethetai=aa0thet(ityp1,ityp2,ityp3)
4210 ccl=cosph1(l)*cosph2(k-l)
4211 ssl=sinph1(l)*sinph2(k-l)
4212 scl=sinph1(l)*cosph2(k-l)
4213 csl=cosph1(l)*sinph2(k-l)
4214 cosph1ph2(l,k)=ccl-ssl
4215 cosph1ph2(k,l)=ccl+ssl
4216 sinph1ph2(l,k)=scl+csl
4217 sinph1ph2(k,l)=scl-csl
4221 write (iout,*) "i",i," ityp1",ityp1," ityp2",ityp2,
4222 & " ityp3",ityp3," theti2",theti2," phii",phii," phii1",phii1
4223 write (iout,*) "coskt and sinkt"
4225 write (iout,*) k,coskt(k),sinkt(k)
4229 ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
4230 dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
4233 & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
4234 & " ethetai",ethetai
4237 write (iout,*) "cosph and sinph"
4239 write (iout,*) k,cosph1(k),sinph1(k),cosph2(k),sinph2(k)
4241 write (iout,*) "cosph1ph2 and sinph2ph2"
4244 write (iout,*) l,k,cosph1ph2(l,k),cosph1ph2(k,l),
4245 & sinph1ph2(l,k),sinph1ph2(k,l)
4248 write(iout,*) "ethetai",ethetai
4252 aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
4253 & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
4254 & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
4255 & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
4256 ethetai=ethetai+sinkt(m)*aux
4257 dethetai=dethetai+0.5d0*m*aux*coskt(m)
4258 dephii=dephii+k*sinkt(m)*(
4259 & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
4260 & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
4261 dephii1=dephii1+k*sinkt(m)*(
4262 & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
4263 & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
4265 & write (iout,*) "m",m," k",k," bbthet",
4266 & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
4267 & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
4268 & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
4269 & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
4273 & write(iout,*) "ethetai",ethetai
4277 aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
4278 & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
4279 & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
4280 & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
4281 ethetai=ethetai+sinkt(m)*aux
4282 dethetai=dethetai+0.5d0*m*coskt(m)*aux
4283 dephii=dephii+l*sinkt(m)*(
4284 & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)-
4285 & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
4286 & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
4287 & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
4288 dephii1=dephii1+(k-l)*sinkt(m)*(
4289 & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
4290 & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
4291 & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
4292 & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
4294 write (iout,*) "m",m," k",k," l",l," ffthet",
4295 & ffthet(l,k,m,ityp1,ityp2,ityp3),
4296 & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
4297 & ggthet(l,k,m,ityp1,ityp2,ityp3),
4298 & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
4299 write (iout,*) cosph1ph2(l,k)*sinkt(m),
4300 & cosph1ph2(k,l)*sinkt(m),
4301 & sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
4308 if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)')
4309 & 'ebe',i,theta(i)*rad2deg,phii*rad2deg,
4310 & phii1*rad2deg,ethetai
4312 etheta=etheta+ethetai
4314 if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
4315 if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
4316 gloc(nphi+i-2,icg)=wang*dethetai
4322 c-----------------------------------------------------------------------------
4323 subroutine esc(escloc)
4324 C Calculate the local energy of a side chain and its derivatives in the
4325 C corresponding virtual-bond valence angles THETA and the spherical angles
4327 implicit real*8 (a-h,o-z)
4328 include 'DIMENSIONS'
4329 include 'DIMENSIONS.ZSCOPT'
4330 include 'COMMON.GEO'
4331 include 'COMMON.LOCAL'
4332 include 'COMMON.VAR'
4333 include 'COMMON.INTERACT'
4334 include 'COMMON.DERIV'
4335 include 'COMMON.CHAIN'
4336 include 'COMMON.IOUNITS'
4337 include 'COMMON.NAMES'
4338 include 'COMMON.FFIELD'
4339 double precision x(3),dersc(3),xemp(3),dersc0(3),dersc1(3),
4340 & ddersc0(3),ddummy(3),xtemp(3),temp(3)
4341 common /sccalc/ time11,time12,time112,theti,it,nlobit
4344 c write (iout,'(a)') 'ESC'
4345 do i=loc_start,loc_end
4347 if (it.eq.10) goto 1
4349 c print *,'i=',i,' it=',it,' nlobit=',nlobit
4350 c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
4351 theti=theta(i+1)-pipol
4355 c write (iout,*) "i",i," x",x(1),x(2),x(3)
4357 if (x(2).gt.pi-delta) then
4361 call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
4363 call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
4364 call spline1(x(2),pi-delta,delta,escloci0,escloci1,dersc0(2),
4366 call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
4367 & ddersc0(1),dersc(1))
4368 call spline2(x(2),pi-delta,delta,dersc0(3),dersc1(3),
4369 & ddersc0(3),dersc(3))
4371 call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
4373 call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
4374 call spline1(x(2),pi-delta,delta,esclocbi0,esclocbi1,
4375 & dersc0(2),esclocbi,dersc02)
4376 call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
4378 call splinthet(x(2),0.5d0*delta,ss,ssd)
4383 dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
4385 dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
4386 c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
4388 escloci=ss*escloci+(1.0d0-ss)*esclocbi
4390 c write (iout,*) escloci
4391 else if (x(2).lt.delta) then
4395 call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
4397 call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
4398 call spline1(x(2),delta,-delta,escloci0,escloci1,dersc0(2),
4400 call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
4401 & ddersc0(1),dersc(1))
4402 call spline2(x(2),delta,-delta,dersc0(3),dersc1(3),
4403 & ddersc0(3),dersc(3))
4405 call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
4407 call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
4408 call spline1(x(2),delta,-delta,esclocbi0,esclocbi1,
4409 & dersc0(2),esclocbi,dersc02)
4410 call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
4415 call splinthet(x(2),0.5d0*delta,ss,ssd)
4417 dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
4419 dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
4420 c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
4422 escloci=ss*escloci+(1.0d0-ss)*esclocbi
4423 c write (iout,*) escloci
4425 call enesc(x,escloci,dersc,ddummy,.false.)
4428 escloc=escloc+escloci
4429 c write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc
4431 gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
4433 gloc(ialph(i,1),icg)=wscloc*dersc(2)
4434 gloc(ialph(i,1)+nside,icg)=wscloc*dersc(3)
4439 C---------------------------------------------------------------------------
4440 subroutine enesc(x,escloci,dersc,ddersc,mixed)
4441 implicit real*8 (a-h,o-z)
4442 include 'DIMENSIONS'
4443 include 'COMMON.GEO'
4444 include 'COMMON.LOCAL'
4445 include 'COMMON.IOUNITS'
4446 common /sccalc/ time11,time12,time112,theti,it,nlobit
4447 double precision x(3),z(3),Ax(3,maxlob,-1:1),dersc(3),ddersc(3)
4448 double precision contr(maxlob,-1:1)
4450 c write (iout,*) 'it=',it,' nlobit=',nlobit
4454 if (mixed) ddersc(j)=0.0d0
4458 C Because of periodicity of the dependence of the SC energy in omega we have
4459 C to add up the contributions from x(3)-2*pi, x(3), and x(3+2*pi).
4460 C To avoid underflows, first compute & store the exponents.
4468 z(k)=x(k)-censc(k,j,it)
4473 Axk=Axk+gaussc(l,k,j,it)*z(l)
4479 expfac=expfac+Ax(k,j,iii)*z(k)
4487 C As in the case of ebend, we want to avoid underflows in exponentiation and
4488 C subsequent NaNs and INFs in energy calculation.
4489 C Find the largest exponent
4493 if (emin.gt.contr(j,iii)) emin=contr(j,iii)
4497 cd print *,'it=',it,' emin=',emin
4499 C Compute the contribution to SC energy and derivatives
4503 expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
4504 cd print *,'j=',j,' expfac=',expfac
4505 escloc_i=escloc_i+expfac
4507 dersc(k)=dersc(k)+Ax(k,j,iii)*expfac
4511 ddersc(k)=ddersc(k)+(-Ax(2,j,iii)*Ax(k,j,iii)
4512 & +gaussc(k,2,j,it))*expfac
4519 dersc(1)=dersc(1)/cos(theti)**2
4520 ddersc(1)=ddersc(1)/cos(theti)**2
4523 escloci=-(dlog(escloc_i)-emin)
4525 dersc(j)=dersc(j)/escloc_i
4529 ddersc(j)=(ddersc(j)/escloc_i+dersc(2)*dersc(j))
4534 C------------------------------------------------------------------------------
4535 subroutine enesc_bound(x,escloci,dersc,dersc12,mixed)
4536 implicit real*8 (a-h,o-z)
4537 include 'DIMENSIONS'
4538 include 'COMMON.GEO'
4539 include 'COMMON.LOCAL'
4540 include 'COMMON.IOUNITS'
4541 common /sccalc/ time11,time12,time112,theti,it,nlobit
4542 double precision x(3),z(3),Ax(3,maxlob),dersc(3)
4543 double precision contr(maxlob)
4554 z(k)=x(k)-censc(k,j,it)
4560 Axk=Axk+gaussc(l,k,j,it)*z(l)
4566 expfac=expfac+Ax(k,j)*z(k)
4571 C As in the case of ebend, we want to avoid underflows in exponentiation and
4572 C subsequent NaNs and INFs in energy calculation.
4573 C Find the largest exponent
4576 if (emin.gt.contr(j)) emin=contr(j)
4580 C Compute the contribution to SC energy and derivatives
4584 expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
4585 escloc_i=escloc_i+expfac
4587 dersc(k)=dersc(k)+Ax(k,j)*expfac
4589 if (mixed) dersc12=dersc12+(-Ax(2,j)*Ax(1,j)
4590 & +gaussc(1,2,j,it))*expfac
4594 dersc(1)=dersc(1)/cos(theti)**2
4595 dersc12=dersc12/cos(theti)**2
4596 escloci=-(dlog(escloc_i)-emin)
4598 dersc(j)=dersc(j)/escloc_i
4600 if (mixed) dersc12=(dersc12/escloc_i+dersc(2)*dersc(1))
4604 c----------------------------------------------------------------------------------
4605 subroutine esc(escloc)
4606 C Calculate the local energy of a side chain and its derivatives in the
4607 C corresponding virtual-bond valence angles THETA and the spherical angles
4608 C ALPHA and OMEGA derived from AM1 all-atom calculations.
4609 C added by Urszula Kozlowska. 07/11/2007
4611 implicit real*8 (a-h,o-z)
4612 include 'DIMENSIONS'
4613 include 'DIMENSIONS.ZSCOPT'
4614 include 'DIMENSIONS.FREE'
4615 include 'COMMON.GEO'
4616 include 'COMMON.LOCAL'
4617 include 'COMMON.VAR'
4618 include 'COMMON.SCROT'
4619 include 'COMMON.INTERACT'
4620 include 'COMMON.DERIV'
4621 include 'COMMON.CHAIN'
4622 include 'COMMON.IOUNITS'
4623 include 'COMMON.NAMES'
4624 include 'COMMON.FFIELD'
4625 include 'COMMON.CONTROL'
4626 include 'COMMON.VECTORS'
4627 double precision x_prime(3),y_prime(3),z_prime(3)
4628 & , sumene,dsc_i,dp2_i,x(65),
4629 & xx,yy,zz,sumene1,sumene2,sumene3,sumene4,s1,s1_6,s2,s2_6,
4630 & de_dxx,de_dyy,de_dzz,de_dt
4631 double precision s1_t,s1_6_t,s2_t,s2_6_t
4633 & dXX_Ci1(3),dYY_Ci1(3),dZZ_Ci1(3),dXX_Ci(3),
4634 & dYY_Ci(3),dZZ_Ci(3),dXX_XYZ(3),dYY_XYZ(3),dZZ_XYZ(3),
4635 & dt_dCi(3),dt_dCi1(3)
4636 common /sccalc/ time11,time12,time112,theti,it,nlobit
4639 do i=loc_start,loc_end
4640 costtab(i+1) =dcos(theta(i+1))
4641 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
4642 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
4643 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
4644 cosfac2=0.5d0/(1.0d0+costtab(i+1))
4645 cosfac=dsqrt(cosfac2)
4646 sinfac2=0.5d0/(1.0d0-costtab(i+1))
4647 sinfac=dsqrt(sinfac2)
4649 if (it.eq.10) goto 1
4651 C Compute the axes of tghe local cartesian coordinates system; store in
4652 c x_prime, y_prime and z_prime
4659 C write(2,*) "dc_norm", dc_norm(1,i+nres),dc_norm(2,i+nres),
4660 C & dc_norm(3,i+nres)
4662 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
4663 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
4666 z_prime(j) = -uz(j,i-1)
4669 c write (2,*) "x_prime",(x_prime(j),j=1,3)
4670 c write (2,*) "y_prime",(y_prime(j),j=1,3)
4671 c write (2,*) "z_prime",(z_prime(j),j=1,3)
4672 c write (2,*) "xx",scalar(x_prime(1),x_prime(1)),
4673 c & " xy",scalar(x_prime(1),y_prime(1)),
4674 c & " xz",scalar(x_prime(1),z_prime(1)),
4675 c & " yy",scalar(y_prime(1),y_prime(1)),
4676 c & " yz",scalar(y_prime(1),z_prime(1)),
4677 c & " zz",scalar(z_prime(1),z_prime(1))
4679 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
4680 C to local coordinate system. Store in xx, yy, zz.
4686 xx = xx + x_prime(j)*dc_norm(j,i+nres)
4687 yy = yy + y_prime(j)*dc_norm(j,i+nres)
4688 zz = zz + z_prime(j)*dc_norm(j,i+nres)
4695 C Compute the energy of the ith side cbain
4697 c write (2,*) "xx",xx," yy",yy," zz",zz
4700 x(j) = sc_parmin(j,it)
4703 Cc diagnostics - remove later
4705 yy1 = dsin(alph(2))*dcos(omeg(2))
4706 zz1 = -dsin(alph(2))*dsin(omeg(2))
4707 write(2,'(3f8.1,3f9.3,1x,3f9.3)')
4708 & alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
4710 C," --- ", xx_w,yy_w,zz_w
4713 sumene1= x(1)+ x(2)*xx+ x(3)*yy+ x(4)*zz+ x(5)*xx**2
4714 & + x(6)*yy**2+ x(7)*zz**2+ x(8)*xx*zz+ x(9)*xx*yy
4716 sumene2= x(11) + x(12)*xx + x(13)*yy + x(14)*zz + x(15)*xx**2
4717 & + x(16)*yy**2 + x(17)*zz**2 + x(18)*xx*zz + x(19)*xx*yy
4719 sumene3= x(21) +x(22)*xx +x(23)*yy +x(24)*zz +x(25)*xx**2
4720 & +x(26)*yy**2 +x(27)*zz**2 +x(28)*xx*zz +x(29)*xx*yy
4721 & +x(30)*yy*zz +x(31)*xx**3 +x(32)*yy**3 +x(33)*zz**3
4722 & +x(34)*(xx**2)*yy +x(35)*(xx**2)*zz +x(36)*(yy**2)*xx
4723 & +x(37)*(yy**2)*zz +x(38)*(zz**2)*xx +x(39)*(zz**2)*yy
4725 sumene4= x(41) +x(42)*xx +x(43)*yy +x(44)*zz +x(45)*xx**2
4726 & +x(46)*yy**2 +x(47)*zz**2 +x(48)*xx*zz +x(49)*xx*yy
4727 & +x(50)*yy*zz +x(51)*xx**3 +x(52)*yy**3 +x(53)*zz**3
4728 & +x(54)*(xx**2)*yy +x(55)*(xx**2)*zz +x(56)*(yy**2)*xx
4729 & +x(57)*(yy**2)*zz +x(58)*(zz**2)*xx +x(59)*(zz**2)*yy
4731 dsc_i = 0.743d0+x(61)
4733 dscp1=dsqrt(dsc_i**2+dp2_i**2-2*dsc_i*dp2_i
4734 & *(xx*cost2tab(i+1)+yy*sint2tab(i+1)))
4735 dscp2=dsqrt(dsc_i**2+dp2_i**2-2*dsc_i*dp2_i
4736 & *(xx*cost2tab(i+1)-yy*sint2tab(i+1)))
4737 s1=(1+x(63))/(0.1d0 + dscp1)
4738 s1_6=(1+x(64))/(0.1d0 + dscp1**6)
4739 s2=(1+x(65))/(0.1d0 + dscp2)
4740 s2_6=(1+x(65))/(0.1d0 + dscp2**6)
4741 sumene = ( sumene3*sint2tab(i+1) + sumene1)*(s1+s1_6)
4742 & + (sumene4*cost2tab(i+1) +sumene2)*(s2+s2_6)
4743 c write(2,'(i2," sumene",7f9.3)') i,sumene1,sumene2,sumene3,
4745 c & dscp1,dscp2,sumene
4746 c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4747 escloc = escloc + sumene
4748 c write (2,*) "escloc",escloc
4749 if (.not. calc_grad) goto 1
4753 C This section to check the numerical derivatives of the energy of ith side
4754 C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert
4755 C #define DEBUG in the code to turn it on.
4757 write (2,*) "sumene =",sumene
4761 write (2,*) xx,yy,zz
4762 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4763 de_dxx_num=(sumenep-sumene)/aincr
4765 write (2,*) "xx+ sumene from enesc=",sumenep
4768 write (2,*) xx,yy,zz
4769 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4770 de_dyy_num=(sumenep-sumene)/aincr
4772 write (2,*) "yy+ sumene from enesc=",sumenep
4775 write (2,*) xx,yy,zz
4776 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4777 de_dzz_num=(sumenep-sumene)/aincr
4779 write (2,*) "zz+ sumene from enesc=",sumenep
4780 costsave=cost2tab(i+1)
4781 sintsave=sint2tab(i+1)
4782 cost2tab(i+1)=dcos(0.5d0*(theta(i+1)+aincr))
4783 sint2tab(i+1)=dsin(0.5d0*(theta(i+1)+aincr))
4784 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4785 de_dt_num=(sumenep-sumene)/aincr
4786 write (2,*) " t+ sumene from enesc=",sumenep
4787 cost2tab(i+1)=costsave
4788 sint2tab(i+1)=sintsave
4789 C End of diagnostics section.
4792 C Compute the gradient of esc
4794 pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2
4795 pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2
4796 pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2
4797 pom_s26=6*(1.0d0+x(65))/(0.1d0 + dscp2**6)**2
4798 pom_dx=dsc_i*dp2_i*cost2tab(i+1)
4799 pom_dy=dsc_i*dp2_i*sint2tab(i+1)
4800 pom_dt1=-0.5d0*dsc_i*dp2_i*(xx*sint2tab(i+1)-yy*cost2tab(i+1))
4801 pom_dt2=-0.5d0*dsc_i*dp2_i*(xx*sint2tab(i+1)+yy*cost2tab(i+1))
4802 pom1=(sumene3*sint2tab(i+1)+sumene1)
4803 & *(pom_s1/dscp1+pom_s16*dscp1**4)
4804 pom2=(sumene4*cost2tab(i+1)+sumene2)
4805 & *(pom_s2/dscp2+pom_s26*dscp2**4)
4806 sumene1x=x(2)+2*x(5)*xx+x(8)*zz+ x(9)*yy
4807 sumene3x=x(22)+2*x(25)*xx+x(28)*zz+x(29)*yy+3*x(31)*xx**2
4808 & +2*x(34)*xx*yy +2*x(35)*xx*zz +x(36)*(yy**2) +x(38)*(zz**2)
4810 sumene2x=x(12)+2*x(15)*xx+x(18)*zz+ x(19)*yy
4811 sumene4x=x(42)+2*x(45)*xx +x(48)*zz +x(49)*yy +3*x(51)*xx**2
4812 & +2*x(54)*xx*yy+2*x(55)*xx*zz+x(56)*(yy**2)+x(58)*(zz**2)
4814 de_dxx =(sumene1x+sumene3x*sint2tab(i+1))*(s1+s1_6)
4815 & +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6)
4816 & +(pom1+pom2)*pom_dx
4818 write(2,*), "de_dxx = ", de_dxx,de_dxx_num
4821 sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz
4822 sumene3y=x(23) +2*x(26)*yy +x(29)*xx +x(30)*zz +3*x(32)*yy**2
4823 & +x(34)*(xx**2) +2*x(36)*yy*xx +2*x(37)*yy*zz +x(39)*(zz**2)
4825 sumene2y=x(13) + 2*x(16)*yy + x(19)*xx + x(20)*zz
4826 sumene4y=x(43)+2*x(46)*yy+x(49)*xx +x(50)*zz
4827 & +3*x(52)*yy**2+x(54)*xx**2+2*x(56)*yy*xx +2*x(57)*yy*zz
4828 & +x(59)*zz**2 +x(60)*xx*zz
4829 de_dyy =(sumene1y+sumene3y*sint2tab(i+1))*(s1+s1_6)
4830 & +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6)
4831 & +(pom1-pom2)*pom_dy
4833 write(2,*), "de_dyy = ", de_dyy,de_dyy_num
4836 de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy
4837 & +3*x(33)*zz**2 +x(35)*xx**2 +x(37)*yy**2 +2*x(38)*zz*xx
4838 & +2*x(39)*zz*yy +x(40)*xx*yy)*sint2tab(i+1)*(s1+s1_6)
4839 & +(x(4) + 2*x(7)*zz+ x(8)*xx + x(10)*yy)*(s1+s1_6)
4840 & +(x(44)+2*x(47)*zz +x(48)*xx +x(50)*yy +3*x(53)*zz**2
4841 & +x(55)*xx**2 +x(57)*(yy**2)+2*x(58)*zz*xx +2*x(59)*zz*yy
4842 & +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6)
4843 & + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6)
4845 write(2,*), "de_dzz = ", de_dzz,de_dzz_num
4848 de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6)
4849 & -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6)
4850 & +pom1*pom_dt1+pom2*pom_dt2
4852 write(2,*), "de_dt = ", de_dt,de_dt_num
4856 cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
4857 cossc1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres))
4858 cosfac2xx=cosfac2*xx
4859 sinfac2yy=sinfac2*yy
4861 dt_dCi(k) = -(dc_norm(k,i-1)+costtab(i+1)*dc_norm(k,i))*
4863 dt_dCi1(k)= -(dc_norm(k,i)+costtab(i+1)*dc_norm(k,i-1))*
4865 pom=(dC_norm(k,i+nres)-cossc*dC_norm(k,i))*vbld_inv(i+1)
4866 pom1=(dC_norm(k,i+nres)-cossc1*dC_norm(k,i-1))*vbld_inv(i)
4867 c write (iout,*) "i",i," k",k," pom",pom," pom1",pom1,
4868 c & " dt_dCi",dt_dCi(k)," dt_dCi1",dt_dCi1(k)
4869 c write (iout,*) "dC_norm",(dC_norm(j,i),j=1,3),
4870 c & (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i)
4871 dXX_Ci(k)=pom*cosfac-dt_dCi(k)*cosfac2xx
4872 dXX_Ci1(k)=-pom1*cosfac-dt_dCi1(k)*cosfac2xx
4873 dYY_Ci(k)=pom*sinfac+dt_dCi(k)*sinfac2yy
4874 dYY_Ci1(k)=pom1*sinfac+dt_dCi1(k)*sinfac2yy
4878 dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
4879 dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
4882 dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
4883 dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
4884 dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
4886 dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
4887 dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
4891 dXX_Ctab(k,i)=dXX_Ci(k)
4892 dXX_C1tab(k,i)=dXX_Ci1(k)
4893 dYY_Ctab(k,i)=dYY_Ci(k)
4894 dYY_C1tab(k,i)=dYY_Ci1(k)
4895 dZZ_Ctab(k,i)=dZZ_Ci(k)
4896 dZZ_C1tab(k,i)=dZZ_Ci1(k)
4897 dXX_XYZtab(k,i)=dXX_XYZ(k)
4898 dYY_XYZtab(k,i)=dYY_XYZ(k)
4899 dZZ_XYZtab(k,i)=dZZ_XYZ(k)
4903 c write (iout,*) "k",k," dxx_ci1",dxx_ci1(k)," dyy_ci1",
4904 c & dyy_ci1(k)," dzz_ci1",dzz_ci1(k)
4905 c write (iout,*) "k",k," dxx_ci",dxx_ci(k)," dyy_ci",
4906 c & dyy_ci(k)," dzz_ci",dzz_ci(k)
4907 c write (iout,*) "k",k," dt_dci",dt_dci(k)," dt_dci",
4909 c write (iout,*) "k",k," dxx_XYZ",dxx_XYZ(k)," dyy_XYZ",
4910 c & dyy_XYZ(k)," dzz_XYZ",dzz_XYZ(k)
4911 gscloc(k,i-1)=gscloc(k,i-1)+de_dxx*dxx_ci1(k)
4912 & +de_dyy*dyy_ci1(k)+de_dzz*dzz_ci1(k)+de_dt*dt_dCi1(k)
4913 gscloc(k,i)=gscloc(k,i)+de_dxx*dxx_Ci(k)
4914 & +de_dyy*dyy_Ci(k)+de_dzz*dzz_Ci(k)+de_dt*dt_dCi(k)
4915 gsclocx(k,i)= de_dxx*dxx_XYZ(k)
4916 & +de_dyy*dyy_XYZ(k)+de_dzz*dzz_XYZ(k)
4918 c write(iout,*) "ENERGY GRAD = ", (gscloc(k,i-1),k=1,3),
4919 c & (gscloc(k,i),k=1,3),(gsclocx(k,i),k=1,3)
4921 C to check gradient call subroutine check_grad
4928 c------------------------------------------------------------------------------
4929 subroutine gcont(rij,r0ij,eps0ij,delta,fcont,fprimcont)
4931 C This procedure calculates two-body contact function g(rij) and its derivative:
4934 C g(rij) = esp0ij*(-0.9375*x+0.625*x**3-0.1875*x**5) ! -1 =< x =< 1
4937 C where x=(rij-r0ij)/delta
4939 C rij - interbody distance, r0ij - contact distance, eps0ij - contact energy
4942 double precision rij,r0ij,eps0ij,fcont,fprimcont
4943 double precision x,x2,x4,delta
4947 if (x.lt.-1.0D0) then
4950 else if (x.le.1.0D0) then
4953 fcont=eps0ij*(x*(-0.9375D0+0.6250D0*x2-0.1875D0*x4)+0.5D0)
4954 fprimcont=eps0ij * (-0.9375D0+1.8750D0*x2-0.9375D0*x4)/delta
4961 c------------------------------------------------------------------------------
4962 subroutine splinthet(theti,delta,ss,ssder)
4963 implicit real*8 (a-h,o-z)
4964 include 'DIMENSIONS'
4965 include 'DIMENSIONS.ZSCOPT'
4966 include 'COMMON.VAR'
4967 include 'COMMON.GEO'
4970 if (theti.gt.pipol) then
4971 call gcont(theti,thetup,1.0d0,delta,ss,ssder)
4973 call gcont(-theti,-thetlow,1.0d0,delta,ss,ssder)
4978 c------------------------------------------------------------------------------
4979 subroutine spline1(x,x0,delta,f0,f1,fprim0,f,fprim)
4981 double precision x,x0,delta,f0,f1,fprim0,f,fprim
4982 double precision ksi,ksi2,ksi3,a1,a2,a3
4983 a1=fprim0*delta/(f1-f0)
4989 f=f0+(f1-f0)*ksi*(a1+ksi*(a2+a3*ksi))
4990 fprim=(f1-f0)/delta*(a1+ksi*(2*a2+3*ksi*a3))
4993 c------------------------------------------------------------------------------
4994 subroutine spline2(x,x0,delta,f0x,f1x,fprim0x,fx)
4996 double precision x,x0,delta,f0x,f1x,fprim0x,fx
4997 double precision ksi,ksi2,ksi3,a1,a2,a3
5002 a2=3*(f1x-f0x)-2*fprim0x*delta
5003 a3=fprim0x*delta-2*(f1x-f0x)
5004 fx=f0x+a1*ksi+a2*ksi2+a3*ksi3
5007 C-----------------------------------------------------------------------------
5009 C-----------------------------------------------------------------------------
5010 subroutine etor(etors,edihcnstr,fact)
5011 implicit real*8 (a-h,o-z)
5012 include 'DIMENSIONS'
5013 include 'DIMENSIONS.ZSCOPT'
5014 include 'COMMON.VAR'
5015 include 'COMMON.GEO'
5016 include 'COMMON.LOCAL'
5017 include 'COMMON.TORSION'
5018 include 'COMMON.INTERACT'
5019 include 'COMMON.DERIV'
5020 include 'COMMON.CHAIN'
5021 include 'COMMON.NAMES'
5022 include 'COMMON.IOUNITS'
5023 include 'COMMON.FFIELD'
5024 include 'COMMON.TORCNSTR'
5026 C Set lprn=.true. for debugging
5030 do i=iphi_start,iphi_end
5031 itori=itortyp(itype(i-2))
5032 itori1=itortyp(itype(i-1))
5035 C Proline-Proline pair is a special case...
5036 if (itori.eq.3 .and. itori1.eq.3) then
5037 if (phii.gt.-dwapi3) then
5039 fac=1.0D0/(1.0D0-cosphi)
5040 etorsi=v1(1,3,3)*fac
5041 etorsi=etorsi+etorsi
5042 etors=etors+etorsi-v1(1,3,3)
5043 gloci=gloci-3*fac*etorsi*dsin(3*phii)
5046 v1ij=v1(j+1,itori,itori1)
5047 v2ij=v2(j+1,itori,itori1)
5050 etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
5051 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5055 v1ij=v1(j,itori,itori1)
5056 v2ij=v2(j,itori,itori1)
5059 etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
5060 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5064 & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
5065 & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
5066 & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
5067 gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
5068 c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
5070 ! 6/20/98 - dihedral angle constraints
5073 itori=idih_constr(i)
5076 if (difi.gt.drange(i)) then
5078 edihcnstr=edihcnstr+0.25d0*ftors*difi**4
5079 gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
5080 else if (difi.lt.-drange(i)) then
5082 edihcnstr=edihcnstr+0.25d0*ftors*difi**4
5083 gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
5085 ! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
5086 ! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
5088 ! write (iout,*) 'edihcnstr',edihcnstr
5091 c------------------------------------------------------------------------------
5093 subroutine etor(etors,edihcnstr,fact)
5094 implicit real*8 (a-h,o-z)
5095 include 'DIMENSIONS'
5096 include 'DIMENSIONS.ZSCOPT'
5097 include 'COMMON.VAR'
5098 include 'COMMON.GEO'
5099 include 'COMMON.LOCAL'
5100 include 'COMMON.TORSION'
5101 include 'COMMON.INTERACT'
5102 include 'COMMON.DERIV'
5103 include 'COMMON.CHAIN'
5104 include 'COMMON.NAMES'
5105 include 'COMMON.IOUNITS'
5106 include 'COMMON.FFIELD'
5107 include 'COMMON.TORCNSTR'
5109 C Set lprn=.true. for debugging
5113 do i=iphi_start,iphi_end
5114 if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
5115 itori=itortyp(itype(i-2))
5116 itori1=itortyp(itype(i-1))
5119 C Regular cosine and sine terms
5120 do j=1,nterm(itori,itori1)
5121 v1ij=v1(j,itori,itori1)
5122 v2ij=v2(j,itori,itori1)
5125 etors=etors+v1ij*cosphi+v2ij*sinphi
5126 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5130 C E = SUM ----------------------------------- - v1
5131 C [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1
5133 cosphi=dcos(0.5d0*phii)
5134 sinphi=dsin(0.5d0*phii)
5135 do j=1,nlor(itori,itori1)
5136 vl1ij=vlor1(j,itori,itori1)
5137 vl2ij=vlor2(j,itori,itori1)
5138 vl3ij=vlor3(j,itori,itori1)
5139 pom=vl2ij*cosphi+vl3ij*sinphi
5140 pom1=1.0d0/(pom*pom+1.0d0)
5141 etors=etors+vl1ij*pom1
5143 gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
5145 C Subtract the constant term
5146 etors=etors-v0(itori,itori1)
5148 & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
5149 & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
5150 & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
5151 gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
5152 c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
5155 ! 6/20/98 - dihedral angle constraints
5158 itori=idih_constr(i)
5160 difi=pinorm(phii-phi0(i))
5162 if (difi.gt.drange(i)) then
5164 edihcnstr=edihcnstr+0.25d0*ftors*difi**4
5165 gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
5166 edihi=0.25d0*ftors*difi**4
5167 else if (difi.lt.-drange(i)) then
5169 edihcnstr=edihcnstr+0.25d0*ftors*difi**4
5170 gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
5171 edihi=0.25d0*ftors*difi**4
5175 c write (iout,'(2i5,4f10.5,e15.5)') i,itori,phii,phi0(i),difi,
5177 ! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
5178 ! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
5180 ! write (iout,*) 'edihcnstr',edihcnstr
5183 c----------------------------------------------------------------------------
5184 subroutine etor_d(etors_d,fact2)
5185 C 6/23/01 Compute double torsional energy
5186 implicit real*8 (a-h,o-z)
5187 include 'DIMENSIONS'
5188 include 'DIMENSIONS.ZSCOPT'
5189 include 'COMMON.VAR'
5190 include 'COMMON.GEO'
5191 include 'COMMON.LOCAL'
5192 include 'COMMON.TORSION'
5193 include 'COMMON.INTERACT'
5194 include 'COMMON.DERIV'
5195 include 'COMMON.CHAIN'
5196 include 'COMMON.NAMES'
5197 include 'COMMON.IOUNITS'
5198 include 'COMMON.FFIELD'
5199 include 'COMMON.TORCNSTR'
5201 C Set lprn=.true. for debugging
5205 do i=iphi_start,iphi_end-1
5206 if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
5208 itori=itortyp(itype(i-2))
5209 itori1=itortyp(itype(i-1))
5210 itori2=itortyp(itype(i))
5215 C Regular cosine and sine terms
5216 do j=1,ntermd_1(itori,itori1,itori2)
5217 v1cij=v1c(1,j,itori,itori1,itori2)
5218 v1sij=v1s(1,j,itori,itori1,itori2)
5219 v2cij=v1c(2,j,itori,itori1,itori2)
5220 v2sij=v1s(2,j,itori,itori1,itori2)
5221 cosphi1=dcos(j*phii)
5222 sinphi1=dsin(j*phii)
5223 cosphi2=dcos(j*phii1)
5224 sinphi2=dsin(j*phii1)
5225 etors_d=etors_d+v1cij*cosphi1+v1sij*sinphi1+
5226 & v2cij*cosphi2+v2sij*sinphi2
5227 gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
5228 gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
5230 do k=2,ntermd_2(itori,itori1,itori2)
5232 v1cdij = v2c(k,l,itori,itori1,itori2)
5233 v2cdij = v2c(l,k,itori,itori1,itori2)
5234 v1sdij = v2s(k,l,itori,itori1,itori2)
5235 v2sdij = v2s(l,k,itori,itori1,itori2)
5236 cosphi1p2=dcos(l*phii+(k-l)*phii1)
5237 cosphi1m2=dcos(l*phii-(k-l)*phii1)
5238 sinphi1p2=dsin(l*phii+(k-l)*phii1)
5239 sinphi1m2=dsin(l*phii-(k-l)*phii1)
5240 etors_d=etors_d+v1cdij*cosphi1p2+v2cdij*cosphi1m2+
5241 & v1sdij*sinphi1p2+v2sdij*sinphi1m2
5242 gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2
5243 & -v1cdij*sinphi1p2-v2cdij*sinphi1m2)
5244 gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2
5245 & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
5248 gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*fact2*gloci1
5249 gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*fact2*gloci2
5255 c------------------------------------------------------------------------------
5256 subroutine eback_sc_corr(esccor)
5257 c 7/21/2007 Correlations between the backbone-local and side-chain-local
5258 c conformational states; temporarily implemented as differences
5259 c between UNRES torsional potentials (dependent on three types of
5260 c residues) and the torsional potentials dependent on all 20 types
5261 c of residues computed from AM1 energy surfaces of terminally-blocked
5262 c amino-acid residues.
5263 implicit real*8 (a-h,o-z)
5264 include 'DIMENSIONS'
5265 include 'DIMENSIONS.ZSCOPT'
5266 include 'DIMENSIONS.FREE'
5267 include 'COMMON.VAR'
5268 include 'COMMON.GEO'
5269 include 'COMMON.LOCAL'
5270 include 'COMMON.TORSION'
5271 include 'COMMON.SCCOR'
5272 include 'COMMON.INTERACT'
5273 include 'COMMON.DERIV'
5274 include 'COMMON.CHAIN'
5275 include 'COMMON.NAMES'
5276 include 'COMMON.IOUNITS'
5277 include 'COMMON.FFIELD'
5278 include 'COMMON.CONTROL'
5280 C Set lprn=.true. for debugging
5283 c write (iout,*) "EBACK_SC_COR",itau_start,itau_end,nterm_sccor
5285 do i=itau_start,itau_end
5287 if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
5288 isccori=isccortyp(itype(i-2))
5289 isccori1=isccortyp(itype(i-1))
5291 cccc Added 9 May 2012
5292 cc Tauangle is torsional engle depending on the value of first digit
5293 c(see comment below)
5294 cc Omicron is flat angle depending on the value of first digit
5295 c(see comment below)
5298 do intertyp=1,3 !intertyp
5299 cc Added 09 May 2012 (Adasko)
5300 cc Intertyp means interaction type of backbone mainchain correlation:
5301 c 1 = SC...Ca...Ca...Ca
5302 c 2 = Ca...Ca...Ca...SC
5303 c 3 = SC...Ca...Ca...SCi
5305 if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
5306 & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
5307 & (itype(i-1).eq.21)))
5308 & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
5309 & .or.(itype(i-2).eq.21)))
5310 & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
5311 & (itype(i-1).eq.21)))) cycle
5312 if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle
5313 if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21))
5315 do j=1,nterm_sccor(isccori,isccori1)
5316 v1ij=v1sccor(j,intertyp,isccori,isccori1)
5317 v2ij=v2sccor(j,intertyp,isccori,isccori1)
5318 cosphi=dcos(j*tauangle(intertyp,i))
5319 sinphi=dsin(j*tauangle(intertyp,i))
5320 esccor=esccor+v1ij*cosphi+v2ij*sinphi
5322 esccor_ii=esccor_ii+v1ij*cosphi+v2ij*sinphi
5324 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5326 gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
5327 c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
5328 c &gloc_sc(intertyp,i-3,icg)
5330 & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
5331 & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
5332 & (v1sccor(j,intertyp,itori,itori1),j=1,6)
5333 & ,(v2sccor(j,intertyp,itori,itori1),j=1,6)
5334 gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
5337 write (iout,*) "i",i,(tauangle(j,i),j=1,3),esccor_ii
5341 c write (iout,*) "W@T@F", gloc_sc(1,i,icg),gloc(i,icg)
5345 c------------------------------------------------------------------------------
5346 subroutine multibody(ecorr)
5347 C This subroutine calculates multi-body contributions to energy following
5348 C the idea of Skolnick et al. If side chains I and J make a contact and
5349 C at the same time side chains I+1 and J+1 make a contact, an extra
5350 C contribution equal to sqrt(eps(i,j)*eps(i+1,j+1)) is added.
5351 implicit real*8 (a-h,o-z)
5352 include 'DIMENSIONS'
5353 include 'COMMON.IOUNITS'
5354 include 'COMMON.DERIV'
5355 include 'COMMON.INTERACT'
5356 include 'COMMON.CONTACTS'
5357 double precision gx(3),gx1(3)
5360 C Set lprn=.true. for debugging
5364 write (iout,'(a)') 'Contact function values:'
5366 write (iout,'(i2,20(1x,i2,f10.5))')
5367 & i,(jcont(j,i),facont(j,i),j=1,num_cont(i))
5382 num_conti=num_cont(i)
5383 num_conti1=num_cont(i1)
5388 if (j1.eq.j+ishift .or. j1.eq.j-ishift) then
5389 cd write(iout,*)'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5390 cd & ' ishift=',ishift
5391 C Contacts I--J and I+ISHIFT--J+-ISHIFT1 occur simultaneously.
5392 C The system gains extra energy.
5393 ecorr=ecorr+esccorr(i,j,i1,j1,jj,kk)
5394 endif ! j1==j+-ishift
5403 c------------------------------------------------------------------------------
5404 double precision function esccorr(i,j,k,l,jj,kk)
5405 implicit real*8 (a-h,o-z)
5406 include 'DIMENSIONS'
5407 include 'COMMON.IOUNITS'
5408 include 'COMMON.DERIV'
5409 include 'COMMON.INTERACT'
5410 include 'COMMON.CONTACTS'
5411 double precision gx(3),gx1(3)
5416 cd write (iout,'(4i5,3f10.5)') i,j,k,l,eij,ekl,-eij*ekl
5417 C Calculate the multi-body contribution to energy.
5418 C Calculate multi-body contributions to the gradient.
5419 cd write (iout,'(2(2i3,3f10.5))')i,j,(gacont(m,jj,i),m=1,3),
5420 cd & k,l,(gacont(m,kk,k),m=1,3)
5422 gx(m) =ekl*gacont(m,jj,i)
5423 gx1(m)=eij*gacont(m,kk,k)
5424 gradxorr(m,i)=gradxorr(m,i)-gx(m)
5425 gradxorr(m,j)=gradxorr(m,j)+gx(m)
5426 gradxorr(m,k)=gradxorr(m,k)-gx1(m)
5427 gradxorr(m,l)=gradxorr(m,l)+gx1(m)
5431 gradcorr(ll,m)=gradcorr(ll,m)+gx(ll)
5436 gradcorr(ll,m)=gradcorr(ll,m)+gx1(ll)
5442 c------------------------------------------------------------------------------
5444 subroutine pack_buffer(dimen1,dimen2,atom,indx,buffer)
5445 implicit real*8 (a-h,o-z)
5446 include 'DIMENSIONS'
5447 integer dimen1,dimen2,atom,indx
5448 double precision buffer(dimen1,dimen2)
5449 double precision zapas
5450 common /contacts_hb/ zapas(3,20,maxres,7),
5451 & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
5452 & num_cont_hb(maxres),jcont_hb(20,maxres)
5453 num_kont=num_cont_hb(atom)
5457 buffer(i,indx+(k-1)*3+j)=zapas(j,i,atom,k)
5460 buffer(i,indx+22)=facont_hb(i,atom)
5461 buffer(i,indx+23)=ees0p(i,atom)
5462 buffer(i,indx+24)=ees0m(i,atom)
5463 buffer(i,indx+25)=dfloat(jcont_hb(i,atom))
5465 buffer(1,indx+26)=dfloat(num_kont)
5468 c------------------------------------------------------------------------------
5469 subroutine unpack_buffer(dimen1,dimen2,atom,indx,buffer)
5470 implicit real*8 (a-h,o-z)
5471 include 'DIMENSIONS'
5472 integer dimen1,dimen2,atom,indx
5473 double precision buffer(dimen1,dimen2)
5474 double precision zapas
5475 common /contacts_hb/ zapas(3,20,maxres,7),
5476 & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
5477 & num_cont_hb(maxres),jcont_hb(20,maxres)
5478 num_kont=buffer(1,indx+26)
5479 num_kont_old=num_cont_hb(atom)
5480 num_cont_hb(atom)=num_kont+num_kont_old
5485 zapas(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j)
5488 facont_hb(ii,atom)=buffer(i,indx+22)
5489 ees0p(ii,atom)=buffer(i,indx+23)
5490 ees0m(ii,atom)=buffer(i,indx+24)
5491 jcont_hb(ii,atom)=buffer(i,indx+25)
5495 c------------------------------------------------------------------------------
5497 subroutine multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
5498 C This subroutine calculates multi-body contributions to hydrogen-bonding
5499 implicit real*8 (a-h,o-z)
5500 include 'DIMENSIONS'
5501 include 'DIMENSIONS.ZSCOPT'
5502 include 'COMMON.IOUNITS'
5504 include 'COMMON.INFO'
5506 include 'COMMON.FFIELD'
5507 include 'COMMON.DERIV'
5508 include 'COMMON.INTERACT'
5509 include 'COMMON.CONTACTS'
5511 parameter (max_cont=maxconts)
5512 parameter (max_dim=2*(8*3+2))
5513 parameter (msglen1=max_cont*max_dim*4)
5514 parameter (msglen2=2*msglen1)
5515 integer source,CorrelType,CorrelID,Error
5516 double precision buffer(max_cont,max_dim)
5518 double precision gx(3),gx1(3)
5521 C Set lprn=.true. for debugging
5526 if (fgProcs.le.1) goto 30
5528 write (iout,'(a)') 'Contact function values:'
5530 write (iout,'(2i3,50(1x,i2,f5.2))')
5531 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5532 & j=1,num_cont_hb(i))
5535 C Caution! Following code assumes that electrostatic interactions concerning
5536 C a given atom are split among at most two processors!
5546 cd write (iout,*) 'MyRank',MyRank,' mm',mm
5549 cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
5550 if (MyRank.gt.0) then
5551 C Send correlation contributions to the preceding processor
5553 nn=num_cont_hb(iatel_s)
5554 call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
5555 cd write (iout,*) 'The BUFFER array:'
5557 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
5559 if (ielstart(iatel_s).gt.iatel_s+ispp) then
5561 call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
5562 C Clear the contacts of the atom passed to the neighboring processor
5563 nn=num_cont_hb(iatel_s+1)
5565 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
5567 num_cont_hb(iatel_s)=0
5569 cd write (iout,*) 'Processor ',MyID,MyRank,
5570 cd & ' is sending correlation contribution to processor',MyID-1,
5571 cd & ' msglen=',msglen
5572 cd write (*,*) 'Processor ',MyID,MyRank,
5573 cd & ' is sending correlation contribution to processor',MyID-1,
5574 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5575 call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
5576 cd write (iout,*) 'Processor ',MyID,
5577 cd & ' has sent correlation contribution to processor',MyID-1,
5578 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5579 cd write (*,*) 'Processor ',MyID,
5580 cd & ' has sent correlation contribution to processor',MyID-1,
5581 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5583 endif ! (MyRank.gt.0)
5587 cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
5588 if (MyRank.lt.fgProcs-1) then
5589 C Receive correlation contributions from the next processor
5591 if (ielend(iatel_e).lt.nct-1) msglen=msglen2
5592 cd write (iout,*) 'Processor',MyID,
5593 cd & ' is receiving correlation contribution from processor',MyID+1,
5594 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5595 cd write (*,*) 'Processor',MyID,
5596 cd & ' is receiving correlation contribution from processor',MyID+1,
5597 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5599 do while (nbytes.le.0)
5600 call mp_probe(MyID+1,CorrelType,nbytes)
5602 cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
5603 call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
5604 cd write (iout,*) 'Processor',MyID,
5605 cd & ' has received correlation contribution from processor',MyID+1,
5606 cd & ' msglen=',msglen,' nbytes=',nbytes
5607 cd write (iout,*) 'The received BUFFER array:'
5609 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
5611 if (msglen.eq.msglen1) then
5612 call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
5613 else if (msglen.eq.msglen2) then
5614 call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
5615 call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
5618 & 'ERROR!!!! message length changed while processing correlations.'
5620 & 'ERROR!!!! message length changed while processing correlations.'
5621 call mp_stopall(Error)
5622 endif ! msglen.eq.msglen1
5623 endif ! MyRank.lt.fgProcs-1
5630 write (iout,'(a)') 'Contact function values:'
5632 write (iout,'(2i3,50(1x,i2,f5.2))')
5633 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5634 & j=1,num_cont_hb(i))
5638 C Remove the loop below after debugging !!!
5645 C Calculate the local-electrostatic correlation terms
5646 do i=iatel_s,iatel_e+1
5648 num_conti=num_cont_hb(i)
5649 num_conti1=num_cont_hb(i+1)
5654 c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5655 c & ' jj=',jj,' kk=',kk
5656 if (j1.eq.j+1 .or. j1.eq.j-1) then
5657 C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
5658 C The system gains extra energy.
5659 ecorr=ecorr+ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
5661 write (iout,*) "ecorr",i,j,i+1,j1,
5662 & ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
5665 else if (j1.eq.j) then
5666 C Contacts I-J and I-(J+1) occur simultaneously.
5667 C The system loses extra energy.
5668 c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
5673 c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5674 c & ' jj=',jj,' kk=',kk
5676 C Contacts I-J and (I+1)-J occur simultaneously.
5677 C The system loses extra energy.
5678 c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
5685 c------------------------------------------------------------------------------
5686 subroutine multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,
5688 C This subroutine calculates multi-body contributions to hydrogen-bonding
5689 implicit real*8 (a-h,o-z)
5690 include 'DIMENSIONS'
5691 include 'DIMENSIONS.ZSCOPT'
5692 include 'COMMON.IOUNITS'
5694 include 'COMMON.INFO'
5696 include 'COMMON.FFIELD'
5697 include 'COMMON.DERIV'
5698 include 'COMMON.INTERACT'
5699 include 'COMMON.CONTACTS'
5701 parameter (max_cont=maxconts)
5702 parameter (max_dim=2*(8*3+2))
5703 parameter (msglen1=max_cont*max_dim*4)
5704 parameter (msglen2=2*msglen1)
5705 integer source,CorrelType,CorrelID,Error
5706 double precision buffer(max_cont,max_dim)
5708 double precision gx(3),gx1(3)
5711 C Set lprn=.true. for debugging
5717 if (fgProcs.le.1) goto 30
5719 write (iout,'(a)') 'Contact function values:'
5721 write (iout,'(2i3,50(1x,i2,f5.2))')
5722 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5723 & j=1,num_cont_hb(i))
5726 C Caution! Following code assumes that electrostatic interactions concerning
5727 C a given atom are split among at most two processors!
5737 cd write (iout,*) 'MyRank',MyRank,' mm',mm
5740 cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
5741 if (MyRank.gt.0) then
5742 C Send correlation contributions to the preceding processor
5744 nn=num_cont_hb(iatel_s)
5745 call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
5746 cd write (iout,*) 'The BUFFER array:'
5748 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
5750 if (ielstart(iatel_s).gt.iatel_s+ispp) then
5752 call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
5753 C Clear the contacts of the atom passed to the neighboring processor
5754 nn=num_cont_hb(iatel_s+1)
5756 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
5758 num_cont_hb(iatel_s)=0
5760 cd write (iout,*) 'Processor ',MyID,MyRank,
5761 cd & ' is sending correlation contribution to processor',MyID-1,
5762 cd & ' msglen=',msglen
5763 cd write (*,*) 'Processor ',MyID,MyRank,
5764 cd & ' is sending correlation contribution to processor',MyID-1,
5765 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5766 call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
5767 cd write (iout,*) 'Processor ',MyID,
5768 cd & ' has sent correlation contribution to processor',MyID-1,
5769 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5770 cd write (*,*) 'Processor ',MyID,
5771 cd & ' has sent correlation contribution to processor',MyID-1,
5772 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5774 endif ! (MyRank.gt.0)
5778 cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
5779 if (MyRank.lt.fgProcs-1) then
5780 C Receive correlation contributions from the next processor
5782 if (ielend(iatel_e).lt.nct-1) msglen=msglen2
5783 cd write (iout,*) 'Processor',MyID,
5784 cd & ' is receiving correlation contribution from processor',MyID+1,
5785 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5786 cd write (*,*) 'Processor',MyID,
5787 cd & ' is receiving correlation contribution from processor',MyID+1,
5788 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5790 do while (nbytes.le.0)
5791 call mp_probe(MyID+1,CorrelType,nbytes)
5793 cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
5794 call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
5795 cd write (iout,*) 'Processor',MyID,
5796 cd & ' has received correlation contribution from processor',MyID+1,
5797 cd & ' msglen=',msglen,' nbytes=',nbytes
5798 cd write (iout,*) 'The received BUFFER array:'
5800 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
5802 if (msglen.eq.msglen1) then
5803 call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
5804 else if (msglen.eq.msglen2) then
5805 call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
5806 call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
5809 & 'ERROR!!!! message length changed while processing correlations.'
5811 & 'ERROR!!!! message length changed while processing correlations.'
5812 call mp_stopall(Error)
5813 endif ! msglen.eq.msglen1
5814 endif ! MyRank.lt.fgProcs-1
5821 write (iout,'(a)') 'Contact function values:'
5823 write (iout,'(2i3,50(1x,i2,f5.2))')
5824 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5825 & j=1,num_cont_hb(i))
5831 C Remove the loop below after debugging !!!
5838 C Calculate the dipole-dipole interaction energies
5839 if (wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) then
5840 do i=iatel_s,iatel_e+1
5841 num_conti=num_cont_hb(i)
5848 C Calculate the local-electrostatic correlation terms
5849 do i=iatel_s,iatel_e+1
5851 num_conti=num_cont_hb(i)
5852 num_conti1=num_cont_hb(i+1)
5857 c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5858 c & ' jj=',jj,' kk=',kk
5859 if (j1.eq.j+1 .or. j1.eq.j-1) then
5860 C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
5861 C The system gains extra energy.
5863 sqd1=dsqrt(d_cont(jj,i))
5864 sqd2=dsqrt(d_cont(kk,i1))
5865 sred_geom = sqd1*sqd2
5866 IF (sred_geom.lt.cutoff_corr) THEN
5867 call gcont(sred_geom,r0_corr,1.0D0,delt_corr,
5869 c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5870 c & ' jj=',jj,' kk=',kk
5871 fac_prim1=0.5d0*sqd2/sqd1*fprimcont
5872 fac_prim2=0.5d0*sqd1/sqd2*fprimcont
5874 g_contij(l,1)=fac_prim1*grij_hb_cont(l,jj,i)
5875 g_contij(l,2)=fac_prim2*grij_hb_cont(l,kk,i1)
5878 cd write (iout,*) 'sred_geom=',sred_geom,
5879 cd & ' ekont=',ekont,' fprim=',fprimcont
5880 call calc_eello(i,j,i+1,j1,jj,kk)
5881 if (wcorr4.gt.0.0d0)
5882 & ecorr=ecorr+eello4(i,j,i+1,j1,jj,kk)
5883 if (wcorr5.gt.0.0d0)
5884 & ecorr5=ecorr5+eello5(i,j,i+1,j1,jj,kk)
5885 c print *,"wcorr5",ecorr5
5886 cd write(2,*)'wcorr6',wcorr6,' wturn6',wturn6
5887 cd write(2,*)'ijkl',i,j,i+1,j1
5888 if (wcorr6.gt.0.0d0 .and. (j.ne.i+4 .or. j1.ne.i+3
5889 & .or. wturn6.eq.0.0d0))then
5890 cd write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1
5891 ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk)
5892 cd write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5,
5893 cd & 'ecorr6=',ecorr6
5894 cd write (iout,'(4e15.5)') sred_geom,
5895 cd & dabs(eello4(i,j,i+1,j1,jj,kk)),
5896 cd & dabs(eello5(i,j,i+1,j1,jj,kk)),
5897 cd & dabs(eello6(i,j,i+1,j1,jj,kk))
5898 else if (wturn6.gt.0.0d0
5899 & .and. (j.eq.i+4 .and. j1.eq.i+3)) then
5900 cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1
5901 eturn6=eturn6+eello_turn6(i,jj,kk)
5902 cd write (2,*) 'multibody_eello:eturn6',eturn6
5906 else if (j1.eq.j) then
5907 C Contacts I-J and I-(J+1) occur simultaneously.
5908 C The system loses extra energy.
5909 c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
5914 c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5915 c & ' jj=',jj,' kk=',kk
5917 C Contacts I-J and (I+1)-J occur simultaneously.
5918 C The system loses extra energy.
5919 c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
5926 c------------------------------------------------------------------------------
5927 double precision function ehbcorr(i,j,k,l,jj,kk,coeffp,coeffm)
5928 implicit real*8 (a-h,o-z)
5929 include 'DIMENSIONS'
5930 include 'COMMON.IOUNITS'
5931 include 'COMMON.DERIV'
5932 include 'COMMON.INTERACT'
5933 include 'COMMON.CONTACTS'
5934 double precision gx(3),gx1(3)
5944 ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl)
5945 cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl)
5946 C Following 4 lines for diagnostics.
5951 cd write (iout,*)'Contacts have occurred for peptide groups',i,j,
5953 cd write (iout,*)'Contacts have occurred for peptide groups',
5954 cd & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
5955 cd & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
5956 C Calculate the multi-body contribution to energy.
5957 ecorr=ecorr+ekont*ees
5959 C Calculate multi-body contributions to the gradient.
5961 ghalf=0.5D0*ees*ekl*gacont_hbr(ll,jj,i)
5962 gradcorr(ll,i)=gradcorr(ll,i)+ghalf
5963 & -ekont*(coeffp*ees0pkl*gacontp_hb1(ll,jj,i)+
5964 & coeffm*ees0mkl*gacontm_hb1(ll,jj,i))
5965 gradcorr(ll,j)=gradcorr(ll,j)+ghalf
5966 & -ekont*(coeffp*ees0pkl*gacontp_hb2(ll,jj,i)+
5967 & coeffm*ees0mkl*gacontm_hb2(ll,jj,i))
5968 ghalf=0.5D0*ees*eij*gacont_hbr(ll,kk,k)
5969 gradcorr(ll,k)=gradcorr(ll,k)+ghalf
5970 & -ekont*(coeffp*ees0pij*gacontp_hb1(ll,kk,k)+
5971 & coeffm*ees0mij*gacontm_hb1(ll,kk,k))
5972 gradcorr(ll,l)=gradcorr(ll,l)+ghalf
5973 & -ekont*(coeffp*ees0pij*gacontp_hb2(ll,kk,k)+
5974 & coeffm*ees0mij*gacontm_hb2(ll,kk,k))
5978 gradcorr(ll,m)=gradcorr(ll,m)+
5979 & ees*ekl*gacont_hbr(ll,jj,i)-
5980 & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+
5981 & coeffm*ees0mkl*gacontm_hb3(ll,jj,i))
5986 gradcorr(ll,m)=gradcorr(ll,m)+
5987 & ees*eij*gacont_hbr(ll,kk,k)-
5988 & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+
5989 & coeffm*ees0mij*gacontm_hb3(ll,kk,k))
5996 C---------------------------------------------------------------------------
5997 subroutine dipole(i,j,jj)
5998 implicit real*8 (a-h,o-z)
5999 include 'DIMENSIONS'
6000 include 'DIMENSIONS.ZSCOPT'
6001 include 'COMMON.IOUNITS'
6002 include 'COMMON.CHAIN'
6003 include 'COMMON.FFIELD'
6004 include 'COMMON.DERIV'
6005 include 'COMMON.INTERACT'
6006 include 'COMMON.CONTACTS'
6007 include 'COMMON.TORSION'
6008 include 'COMMON.VAR'
6009 include 'COMMON.GEO'
6010 dimension dipi(2,2),dipj(2,2),dipderi(2),dipderj(2),auxvec(2),
6012 iti1 = itortyp(itype(i+1))
6013 if (j.lt.nres-1) then
6014 itj1 = itortyp(itype(j+1))
6019 dipi(iii,1)=Ub2(iii,i)
6020 dipderi(iii)=Ub2der(iii,i)
6021 dipi(iii,2)=b1(iii,iti1)
6022 dipj(iii,1)=Ub2(iii,j)
6023 dipderj(iii)=Ub2der(iii,j)
6024 dipj(iii,2)=b1(iii,itj1)
6028 call matvec2(a_chuj(1,1,jj,i),dipj(1,iii),auxvec(1))
6031 dip(kkk,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
6034 if (.not.calc_grad) return
6039 call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),dipj(1,iii),
6043 dipderx(lll,kkk,mmm,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
6048 call transpose2(a_chuj(1,1,jj,i),auxmat(1,1))
6049 call matvec2(auxmat(1,1),dipderi(1),auxvec(1))
6051 dipderg(iii,jj,i)=scalar2(auxvec(1),dipj(1,iii))
6053 call matvec2(a_chuj(1,1,jj,i),dipderj(1),auxvec(1))
6055 dipderg(iii+2,jj,i)=scalar2(auxvec(1),dipi(1,iii))
6059 C---------------------------------------------------------------------------
6060 subroutine calc_eello(i,j,k,l,jj,kk)
6062 C This subroutine computes matrices and vectors needed to calculate
6063 C the fourth-, fifth-, and sixth-order local-electrostatic terms.
6065 implicit real*8 (a-h,o-z)
6066 include 'DIMENSIONS'
6067 include 'DIMENSIONS.ZSCOPT'
6068 include 'COMMON.IOUNITS'
6069 include 'COMMON.CHAIN'
6070 include 'COMMON.DERIV'
6071 include 'COMMON.INTERACT'
6072 include 'COMMON.CONTACTS'
6073 include 'COMMON.TORSION'
6074 include 'COMMON.VAR'
6075 include 'COMMON.GEO'
6076 include 'COMMON.FFIELD'
6077 double precision aa1(2,2),aa2(2,2),aa1t(2,2),aa2t(2,2),
6078 & aa1tder(2,2,3,5),aa2tder(2,2,3,5),auxmat(2,2)
6081 cd write (iout,*) 'calc_eello: i=',i,' j=',j,' k=',k,' l=',l,
6082 cd & ' jj=',jj,' kk=',kk
6083 cd if (i.ne.2 .or. j.ne.4 .or. k.ne.3 .or. l.ne.5) return
6086 aa1(iii,jjj)=a_chuj(iii,jjj,jj,i)
6087 aa2(iii,jjj)=a_chuj(iii,jjj,kk,k)
6090 call transpose2(aa1(1,1),aa1t(1,1))
6091 call transpose2(aa2(1,1),aa2t(1,1))
6094 call transpose2(a_chuj_der(1,1,lll,kkk,jj,i),
6095 & aa1tder(1,1,lll,kkk))
6096 call transpose2(a_chuj_der(1,1,lll,kkk,kk,k),
6097 & aa2tder(1,1,lll,kkk))
6101 C parallel orientation of the two CA-CA-CA frames.
6103 iti=itortyp(itype(i))
6107 itk1=itortyp(itype(k+1))
6108 itj=itortyp(itype(j))
6109 if (l.lt.nres-1) then
6110 itl1=itortyp(itype(l+1))
6114 C A1 kernel(j+1) A2T
6116 cd write (iout,'(3f10.5,5x,3f10.5)')
6117 cd & (EUg(iii,jjj,k),jjj=1,2),(EUg(iii,jjj,l),jjj=1,2)
6119 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6120 & aa2tder(1,1,1,1),1,.false.,EUg(1,1,l),EUgder(1,1,l),
6121 & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
6122 C Following matrices are needed only for 6-th order cumulants
6123 IF (wcorr6.gt.0.0d0) THEN
6124 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6125 & aa2tder(1,1,1,1),1,.false.,EUgC(1,1,l),EUgCder(1,1,l),
6126 & AECA(1,1,1),AECAderg(1,1,1),AECAderx(1,1,1,1,1,1))
6127 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6128 & aa2tder(1,1,1,1),2,.false.,Ug2DtEUg(1,1,l),
6129 & Ug2DtEUgder(1,1,1,l),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
6130 & ADtEAderx(1,1,1,1,1,1))
6132 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6133 & aa2tder(1,1,1,1),2,.false.,DtUg2EUg(1,1,l),
6134 & DtUg2EUgder(1,1,1,l),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
6135 & ADtEA1derx(1,1,1,1,1,1))
6137 C End 6-th order cumulants
6140 cd write (2,*) 'In calc_eello6'
6142 cd write (2,*) 'iii=',iii
6144 cd write (2,*) 'kkk=',kkk
6146 cd write (2,'(3(2f10.5),5x)')
6147 cd & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
6152 call transpose2(EUgder(1,1,k),auxmat(1,1))
6153 call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
6154 call transpose2(EUg(1,1,k),auxmat(1,1))
6155 call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
6156 call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
6160 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
6161 & EAEAderx(1,1,lll,kkk,iii,1))
6165 C A1T kernel(i+1) A2
6166 call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
6167 & a_chuj_der(1,1,1,1,kk,k),1,.false.,EUg(1,1,k),EUgder(1,1,k),
6168 & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
6169 C Following matrices are needed only for 6-th order cumulants
6170 IF (wcorr6.gt.0.0d0) THEN
6171 call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
6172 & a_chuj_der(1,1,1,1,kk,k),1,.false.,EUgC(1,1,k),EUgCder(1,1,k),
6173 & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
6174 call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
6175 & a_chuj_der(1,1,1,1,kk,k),2,.false.,Ug2DtEUg(1,1,k),
6176 & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
6177 & ADtEAderx(1,1,1,1,1,2))
6178 call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
6179 & a_chuj_der(1,1,1,1,kk,k),2,.false.,DtUg2EUg(1,1,k),
6180 & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
6181 & ADtEA1derx(1,1,1,1,1,2))
6183 C End 6-th order cumulants
6184 call transpose2(EUgder(1,1,l),auxmat(1,1))
6185 call matmat2(auxmat(1,1),AEA(1,1,2),EAEAderg(1,1,1,2))
6186 call transpose2(EUg(1,1,l),auxmat(1,1))
6187 call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
6188 call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
6192 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6193 & EAEAderx(1,1,lll,kkk,iii,2))
6198 C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
6199 C They are needed only when the fifth- or the sixth-order cumulants are
6201 IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN
6202 call transpose2(AEA(1,1,1),auxmat(1,1))
6203 call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
6204 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
6205 call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
6206 call transpose2(AEAderg(1,1,1),auxmat(1,1))
6207 call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
6208 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
6209 call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
6210 call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
6211 call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
6212 call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
6213 call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
6214 call transpose2(AEA(1,1,2),auxmat(1,1))
6215 call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2))
6216 call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2))
6217 call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2))
6218 call transpose2(AEAderg(1,1,2),auxmat(1,1))
6219 call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2))
6220 call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2))
6221 call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2))
6222 call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2))
6223 call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2))
6224 call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2))
6225 call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2))
6226 C Calculate the Cartesian derivatives of the vectors.
6230 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
6231 call matvec2(auxmat(1,1),b1(1,iti),
6232 & AEAb1derx(1,lll,kkk,iii,1,1))
6233 call matvec2(auxmat(1,1),Ub2(1,i),
6234 & AEAb2derx(1,lll,kkk,iii,1,1))
6235 call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
6236 & AEAb1derx(1,lll,kkk,iii,2,1))
6237 call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
6238 & AEAb2derx(1,lll,kkk,iii,2,1))
6239 call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
6240 call matvec2(auxmat(1,1),b1(1,itj),
6241 & AEAb1derx(1,lll,kkk,iii,1,2))
6242 call matvec2(auxmat(1,1),Ub2(1,j),
6243 & AEAb2derx(1,lll,kkk,iii,1,2))
6244 call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
6245 & AEAb1derx(1,lll,kkk,iii,2,2))
6246 call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1),
6247 & AEAb2derx(1,lll,kkk,iii,2,2))
6254 C Antiparallel orientation of the two CA-CA-CA frames.
6256 iti=itortyp(itype(i))
6260 itk1=itortyp(itype(k+1))
6261 itl=itortyp(itype(l))
6262 itj=itortyp(itype(j))
6263 if (j.lt.nres-1) then
6264 itj1=itortyp(itype(j+1))
6268 C A2 kernel(j-1)T A1T
6269 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6270 & aa2tder(1,1,1,1),1,.true.,EUg(1,1,j),EUgder(1,1,j),
6271 & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
6272 C Following matrices are needed only for 6-th order cumulants
6273 IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
6274 & j.eq.i+4 .and. l.eq.i+3)) THEN
6275 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6276 & aa2tder(1,1,1,1),1,.true.,EUgC(1,1,j),EUgCder(1,1,j),
6277 & AECA(1,1,1),AECAderg(1,1,1),AECAderx(1,1,1,1,1,1))
6278 call kernel(aa2(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6279 & aa2tder(1,1,1,1),2,.true.,Ug2DtEUg(1,1,j),
6280 & Ug2DtEUgder(1,1,1,j),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
6281 & ADtEAderx(1,1,1,1,1,1))
6282 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6283 & aa2tder(1,1,1,1),2,.true.,DtUg2EUg(1,1,j),
6284 & DtUg2EUgder(1,1,1,j),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
6285 & ADtEA1derx(1,1,1,1,1,1))
6287 C End 6-th order cumulants
6288 call transpose2(EUgder(1,1,k),auxmat(1,1))
6289 call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
6290 call transpose2(EUg(1,1,k),auxmat(1,1))
6291 call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
6292 call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
6296 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
6297 & EAEAderx(1,1,lll,kkk,iii,1))
6301 C A2T kernel(i+1)T A1
6302 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6303 & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUg(1,1,k),EUgder(1,1,k),
6304 & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
6305 C Following matrices are needed only for 6-th order cumulants
6306 IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
6307 & j.eq.i+4 .and. l.eq.i+3)) THEN
6308 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6309 & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUgC(1,1,k),EUgCder(1,1,k),
6310 & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
6311 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6312 & a_chuj_der(1,1,1,1,jj,i),2,.true.,Ug2DtEUg(1,1,k),
6313 & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
6314 & ADtEAderx(1,1,1,1,1,2))
6315 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6316 & a_chuj_der(1,1,1,1,jj,i),2,.true.,DtUg2EUg(1,1,k),
6317 & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
6318 & ADtEA1derx(1,1,1,1,1,2))
6320 C End 6-th order cumulants
6321 call transpose2(EUgder(1,1,j),auxmat(1,1))
6322 call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,2,2))
6323 call transpose2(EUg(1,1,j),auxmat(1,1))
6324 call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
6325 call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
6329 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6330 & EAEAderx(1,1,lll,kkk,iii,2))
6335 C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
6336 C They are needed only when the fifth- or the sixth-order cumulants are
6338 IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or.
6339 & (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN
6340 call transpose2(AEA(1,1,1),auxmat(1,1))
6341 call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
6342 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
6343 call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
6344 call transpose2(AEAderg(1,1,1),auxmat(1,1))
6345 call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
6346 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
6347 call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
6348 call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
6349 call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
6350 call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
6351 call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
6352 call transpose2(AEA(1,1,2),auxmat(1,1))
6353 call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2))
6354 call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2))
6355 call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2))
6356 call transpose2(AEAderg(1,1,2),auxmat(1,1))
6357 call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2))
6358 call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2))
6359 call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2))
6360 call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2))
6361 call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2))
6362 call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2))
6363 call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2))
6364 C Calculate the Cartesian derivatives of the vectors.
6368 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
6369 call matvec2(auxmat(1,1),b1(1,iti),
6370 & AEAb1derx(1,lll,kkk,iii,1,1))
6371 call matvec2(auxmat(1,1),Ub2(1,i),
6372 & AEAb2derx(1,lll,kkk,iii,1,1))
6373 call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
6374 & AEAb1derx(1,lll,kkk,iii,2,1))
6375 call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
6376 & AEAb2derx(1,lll,kkk,iii,2,1))
6377 call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
6378 call matvec2(auxmat(1,1),b1(1,itl),
6379 & AEAb1derx(1,lll,kkk,iii,1,2))
6380 call matvec2(auxmat(1,1),Ub2(1,l),
6381 & AEAb2derx(1,lll,kkk,iii,1,2))
6382 call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1),
6383 & AEAb1derx(1,lll,kkk,iii,2,2))
6384 call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j),
6385 & AEAb2derx(1,lll,kkk,iii,2,2))
6394 C---------------------------------------------------------------------------
6395 subroutine kernel(aa1,aa2t,aa1derx,aa2tderx,nderg,transp,
6396 & KK,KKderg,AKA,AKAderg,AKAderx)
6400 double precision aa1(2,2),aa2t(2,2),aa1derx(2,2,3,5),
6401 & aa2tderx(2,2,3,5),KK(2,2),KKderg(2,2,nderg),AKA(2,2),
6402 & AKAderg(2,2,nderg),AKAderx(2,2,3,5,2)
6407 call prodmat3(aa1(1,1),aa2t(1,1),KK(1,1),transp,AKA(1,1))
6409 call prodmat3(aa1(1,1),aa2t(1,1),KKderg(1,1,iii),transp,
6412 cd if (lprn) write (2,*) 'In kernel'
6414 cd if (lprn) write (2,*) 'kkk=',kkk
6416 call prodmat3(aa1derx(1,1,lll,kkk),aa2t(1,1),
6417 & KK(1,1),transp,AKAderx(1,1,lll,kkk,1))
6419 cd write (2,*) 'lll=',lll
6420 cd write (2,*) 'iii=1'
6422 cd write (2,'(3(2f10.5),5x)')
6423 cd & (AKAderx(jjj,mmm,lll,kkk,1),mmm=1,2)
6426 call prodmat3(aa1(1,1),aa2tderx(1,1,lll,kkk),
6427 & KK(1,1),transp,AKAderx(1,1,lll,kkk,2))
6429 cd write (2,*) 'lll=',lll
6430 cd write (2,*) 'iii=2'
6432 cd write (2,'(3(2f10.5),5x)')
6433 cd & (AKAderx(jjj,mmm,lll,kkk,2),mmm=1,2)
6440 C---------------------------------------------------------------------------
6441 double precision function eello4(i,j,k,l,jj,kk)
6442 implicit real*8 (a-h,o-z)
6443 include 'DIMENSIONS'
6444 include 'DIMENSIONS.ZSCOPT'
6445 include 'COMMON.IOUNITS'
6446 include 'COMMON.CHAIN'
6447 include 'COMMON.DERIV'
6448 include 'COMMON.INTERACT'
6449 include 'COMMON.CONTACTS'
6450 include 'COMMON.TORSION'
6451 include 'COMMON.VAR'
6452 include 'COMMON.GEO'
6453 double precision pizda(2,2),ggg1(3),ggg2(3)
6454 cd if (i.ne.1 .or. j.ne.5 .or. k.ne.2 .or.l.ne.4) then
6458 cd print *,'eello4:',i,j,k,l,jj,kk
6459 cd write (2,*) 'i',i,' j',j,' k',k,' l',l
6460 cd call checkint4(i,j,k,l,jj,kk,eel4_num)
6461 cold eij=facont_hb(jj,i)
6462 cold ekl=facont_hb(kk,k)
6464 eel4=-EAEA(1,1,1)-EAEA(2,2,1)
6466 cd eel41=-EAEA(1,1,2)-EAEA(2,2,2)
6467 gcorr_loc(k-1)=gcorr_loc(k-1)
6468 & -ekont*(EAEAderg(1,1,1,1)+EAEAderg(2,2,1,1))
6470 gcorr_loc(l-1)=gcorr_loc(l-1)
6471 & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
6473 gcorr_loc(j-1)=gcorr_loc(j-1)
6474 & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
6479 derx(lll,kkk,iii)=-EAEAderx(1,1,lll,kkk,iii,1)
6480 & -EAEAderx(2,2,lll,kkk,iii,1)
6481 cd derx(lll,kkk,iii)=0.0d0
6485 cd gcorr_loc(l-1)=0.0d0
6486 cd gcorr_loc(j-1)=0.0d0
6487 cd gcorr_loc(k-1)=0.0d0
6489 cd write (iout,*)'Contacts have occurred for peptide groups',
6490 cd & i,j,' fcont:',eij,' eij',' and ',k,l,
6491 cd & ' fcont ',ekl,' eel4=',eel4,' eel4_num',16*eel4_num
6492 if (j.lt.nres-1) then
6499 if (l.lt.nres-1) then
6507 cold ghalf=0.5d0*eel4*ekl*gacont_hbr(ll,jj,i)
6508 ggg1(ll)=eel4*g_contij(ll,1)
6509 ggg2(ll)=eel4*g_contij(ll,2)
6510 ghalf=0.5d0*ggg1(ll)
6512 gradcorr(ll,i)=gradcorr(ll,i)+ghalf+ekont*derx(ll,2,1)
6513 gradcorr(ll,i+1)=gradcorr(ll,i+1)+ekont*derx(ll,3,1)
6514 gradcorr(ll,j)=gradcorr(ll,j)+ghalf+ekont*derx(ll,4,1)
6515 gradcorr(ll,j1)=gradcorr(ll,j1)+ekont*derx(ll,5,1)
6516 cold ghalf=0.5d0*eel4*eij*gacont_hbr(ll,kk,k)
6517 ghalf=0.5d0*ggg2(ll)
6519 gradcorr(ll,k)=gradcorr(ll,k)+ghalf+ekont*derx(ll,2,2)
6520 gradcorr(ll,k+1)=gradcorr(ll,k+1)+ekont*derx(ll,3,2)
6521 gradcorr(ll,l)=gradcorr(ll,l)+ghalf+ekont*derx(ll,4,2)
6522 gradcorr(ll,l1)=gradcorr(ll,l1)+ekont*derx(ll,5,2)
6527 cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*ekl*gacont_hbr(ll,jj,i)
6528 gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll)
6533 cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*eij*gacont_hbr(ll,kk,k)
6534 gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll)
6540 gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1)
6545 gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2)
6549 cd write (2,*) iii,gcorr_loc(iii)
6553 cd write (2,*) 'ekont',ekont
6554 cd write (iout,*) 'eello4',ekont*eel4
6557 C---------------------------------------------------------------------------
6558 double precision function eello5(i,j,k,l,jj,kk)
6559 implicit real*8 (a-h,o-z)
6560 include 'DIMENSIONS'
6561 include 'DIMENSIONS.ZSCOPT'
6562 include 'COMMON.IOUNITS'
6563 include 'COMMON.CHAIN'
6564 include 'COMMON.DERIV'
6565 include 'COMMON.INTERACT'
6566 include 'COMMON.CONTACTS'
6567 include 'COMMON.TORSION'
6568 include 'COMMON.VAR'
6569 include 'COMMON.GEO'
6570 double precision pizda(2,2),auxmat(2,2),auxmat1(2,2),vv(2)
6571 double precision ggg1(3),ggg2(3)
6572 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6577 C /l\ / \ \ / \ / \ / C
6578 C / \ / \ \ / \ / \ / C
6579 C j| o |l1 | o | o| o | | o |o C
6580 C \ |/k\| |/ \| / |/ \| |/ \| C
6581 C \i/ \ / \ / / \ / \ C
6583 C (I) (II) (III) (IV) C
6585 C eello5_1 eello5_2 eello5_3 eello5_4 C
6587 C Antiparallel chains C
6590 C /j\ / \ \ / \ / \ / C
6591 C / \ / \ \ / \ / \ / C
6592 C j1| o |l | o | o| o | | o |o C
6593 C \ |/k\| |/ \| / |/ \| |/ \| C
6594 C \i/ \ / \ / / \ / \ C
6596 C (I) (II) (III) (IV) C
6598 C eello5_1 eello5_2 eello5_3 eello5_4 C
6600 C o denotes a local interaction, vertical lines an electrostatic interaction. C
6602 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6603 cd if (i.ne.2 .or. j.ne.6 .or. k.ne.3 .or. l.ne.5) then
6608 cd & 'EELLO5: Contacts have occurred for peptide groups',i,j,
6610 itk=itortyp(itype(k))
6611 itl=itortyp(itype(l))
6612 itj=itortyp(itype(j))
6617 cd call checkint5(i,j,k,l,jj,kk,eel5_1_num,eel5_2_num,
6618 cd & eel5_3_num,eel5_4_num)
6622 derx(lll,kkk,iii)=0.0d0
6626 cd eij=facont_hb(jj,i)
6627 cd ekl=facont_hb(kk,k)
6629 cd write (iout,*)'Contacts have occurred for peptide groups',
6630 cd & i,j,' fcont:',eij,' eij',' and ',k,l
6632 C Contribution from the graph I.
6633 cd write (2,*) 'AEA ',AEA(1,1,1),AEA(2,1,1),AEA(1,2,1),AEA(2,2,1)
6634 cd write (2,*) 'AEAb2',AEAb2(1,1,1),AEAb2(2,1,1)
6635 call transpose2(EUg(1,1,k),auxmat(1,1))
6636 call matmat2(AEA(1,1,1),auxmat(1,1),pizda(1,1))
6637 vv(1)=pizda(1,1)-pizda(2,2)
6638 vv(2)=pizda(1,2)+pizda(2,1)
6639 eello5_1=scalar2(AEAb2(1,1,1),Ub2(1,k))
6640 & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
6642 C Explicit gradient in virtual-dihedral angles.
6643 if (i.gt.1) g_corr5_loc(i-1)=g_corr5_loc(i-1)
6644 & +ekont*(scalar2(AEAb2derg(1,2,1,1),Ub2(1,k))
6645 & +0.5d0*scalar2(vv(1),Dtobr2der(1,i)))
6646 call transpose2(EUgder(1,1,k),auxmat1(1,1))
6647 call matmat2(AEA(1,1,1),auxmat1(1,1),pizda(1,1))
6648 vv(1)=pizda(1,1)-pizda(2,2)
6649 vv(2)=pizda(1,2)+pizda(2,1)
6650 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6651 & +ekont*(scalar2(AEAb2(1,1,1),Ub2der(1,k))
6652 & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
6653 call matmat2(AEAderg(1,1,1),auxmat(1,1),pizda(1,1))
6654 vv(1)=pizda(1,1)-pizda(2,2)
6655 vv(2)=pizda(1,2)+pizda(2,1)
6657 if (l.lt.nres-1) g_corr5_loc(l-1)=g_corr5_loc(l-1)
6658 & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
6659 & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
6661 if (j.lt.nres-1) g_corr5_loc(j-1)=g_corr5_loc(j-1)
6662 & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
6663 & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
6665 C Cartesian gradient
6669 call matmat2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1),
6671 vv(1)=pizda(1,1)-pizda(2,2)
6672 vv(2)=pizda(1,2)+pizda(2,1)
6673 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6674 & +scalar2(AEAb2derx(1,lll,kkk,iii,1,1),Ub2(1,k))
6675 & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
6682 C Contribution from graph II
6683 call transpose2(EE(1,1,itk),auxmat(1,1))
6684 call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1))
6685 vv(1)=pizda(1,1)+pizda(2,2)
6686 vv(2)=pizda(2,1)-pizda(1,2)
6687 eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk))
6688 & -0.5d0*scalar2(vv(1),Ctobr(1,k))
6690 C Explicit gradient in virtual-dihedral angles.
6691 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6692 & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,k))
6693 call matmat2(auxmat(1,1),AEAderg(1,1,1),pizda(1,1))
6694 vv(1)=pizda(1,1)+pizda(2,2)
6695 vv(2)=pizda(2,1)-pizda(1,2)
6697 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6698 & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
6699 & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
6701 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6702 & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
6703 & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
6705 C Cartesian gradient
6709 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
6711 vv(1)=pizda(1,1)+pizda(2,2)
6712 vv(2)=pizda(2,1)-pizda(1,2)
6713 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6714 & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk))
6715 & -0.5d0*scalar2(vv(1),Ctobr(1,k))
6724 C Parallel orientation
6725 C Contribution from graph III
6726 call transpose2(EUg(1,1,l),auxmat(1,1))
6727 call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
6728 vv(1)=pizda(1,1)-pizda(2,2)
6729 vv(2)=pizda(1,2)+pizda(2,1)
6730 eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,l))
6731 & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
6733 C Explicit gradient in virtual-dihedral angles.
6734 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6735 & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,l))
6736 & +0.5d0*scalar2(vv(1),Dtobr2der(1,j)))
6737 call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
6738 vv(1)=pizda(1,1)-pizda(2,2)
6739 vv(2)=pizda(1,2)+pizda(2,1)
6740 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6741 & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,l))
6742 & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
6743 call transpose2(EUgder(1,1,l),auxmat1(1,1))
6744 call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
6745 vv(1)=pizda(1,1)-pizda(2,2)
6746 vv(2)=pizda(1,2)+pizda(2,1)
6747 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6748 & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,l))
6749 & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
6750 C Cartesian gradient
6754 call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
6756 vv(1)=pizda(1,1)-pizda(2,2)
6757 vv(2)=pizda(1,2)+pizda(2,1)
6758 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6759 & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,l))
6760 & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
6766 C Contribution from graph IV
6768 call transpose2(EE(1,1,itl),auxmat(1,1))
6769 call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
6770 vv(1)=pizda(1,1)+pizda(2,2)
6771 vv(2)=pizda(2,1)-pizda(1,2)
6772 eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl))
6773 & -0.5d0*scalar2(vv(1),Ctobr(1,l))
6775 C Explicit gradient in virtual-dihedral angles.
6776 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6777 & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,l))
6778 call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
6779 vv(1)=pizda(1,1)+pizda(2,2)
6780 vv(2)=pizda(2,1)-pizda(1,2)
6781 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6782 & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl))
6783 & -0.5d0*scalar2(vv(1),Ctobr(1,l)))
6784 C Cartesian gradient
6788 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6790 vv(1)=pizda(1,1)+pizda(2,2)
6791 vv(2)=pizda(2,1)-pizda(1,2)
6792 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6793 & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl))
6794 & -0.5d0*scalar2(vv(1),Ctobr(1,l))
6800 C Antiparallel orientation
6801 C Contribution from graph III
6803 call transpose2(EUg(1,1,j),auxmat(1,1))
6804 call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
6805 vv(1)=pizda(1,1)-pizda(2,2)
6806 vv(2)=pizda(1,2)+pizda(2,1)
6807 eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,j))
6808 & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
6810 C Explicit gradient in virtual-dihedral angles.
6811 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6812 & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,j))
6813 & +0.5d0*scalar2(vv(1),Dtobr2der(1,l)))
6814 call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
6815 vv(1)=pizda(1,1)-pizda(2,2)
6816 vv(2)=pizda(1,2)+pizda(2,1)
6817 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6818 & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,j))
6819 & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
6820 call transpose2(EUgder(1,1,j),auxmat1(1,1))
6821 call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
6822 vv(1)=pizda(1,1)-pizda(2,2)
6823 vv(2)=pizda(1,2)+pizda(2,1)
6824 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6825 & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,j))
6826 & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
6827 C Cartesian gradient
6831 call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
6833 vv(1)=pizda(1,1)-pizda(2,2)
6834 vv(2)=pizda(1,2)+pizda(2,1)
6835 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
6836 & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,j))
6837 & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
6843 C Contribution from graph IV
6845 call transpose2(EE(1,1,itj),auxmat(1,1))
6846 call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
6847 vv(1)=pizda(1,1)+pizda(2,2)
6848 vv(2)=pizda(2,1)-pizda(1,2)
6849 eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj))
6850 & -0.5d0*scalar2(vv(1),Ctobr(1,j))
6852 C Explicit gradient in virtual-dihedral angles.
6853 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6854 & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,j))
6855 call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
6856 vv(1)=pizda(1,1)+pizda(2,2)
6857 vv(2)=pizda(2,1)-pizda(1,2)
6858 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6859 & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj))
6860 & -0.5d0*scalar2(vv(1),Ctobr(1,j)))
6861 C Cartesian gradient
6865 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6867 vv(1)=pizda(1,1)+pizda(2,2)
6868 vv(2)=pizda(2,1)-pizda(1,2)
6869 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
6870 & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj))
6871 & -0.5d0*scalar2(vv(1),Ctobr(1,j))
6878 eel5=eello5_1+eello5_2+eello5_3+eello5_4
6879 cd if (i.eq.2 .and. j.eq.8 .and. k.eq.3 .and. l.eq.7) then
6880 cd write (2,*) 'ijkl',i,j,k,l
6881 cd write (2,*) 'eello5_1',eello5_1,' eello5_2',eello5_2,
6882 cd & ' eello5_3',eello5_3,' eello5_4',eello5_4
6884 cd write(iout,*) 'eello5_1',eello5_1,' eel5_1_num',16*eel5_1_num
6885 cd write(iout,*) 'eello5_2',eello5_2,' eel5_2_num',16*eel5_2_num
6886 cd write(iout,*) 'eello5_3',eello5_3,' eel5_3_num',16*eel5_3_num
6887 cd write(iout,*) 'eello5_4',eello5_4,' eel5_4_num',16*eel5_4_num
6889 if (j.lt.nres-1) then
6896 if (l.lt.nres-1) then
6906 cd write (2,*) 'eij',eij,' ekl',ekl,' ekont',ekont
6908 ggg1(ll)=eel5*g_contij(ll,1)
6909 ggg2(ll)=eel5*g_contij(ll,2)
6910 cold ghalf=0.5d0*eel5*ekl*gacont_hbr(ll,jj,i)
6911 ghalf=0.5d0*ggg1(ll)
6913 gradcorr5(ll,i)=gradcorr5(ll,i)+ghalf+ekont*derx(ll,2,1)
6914 gradcorr5(ll,i+1)=gradcorr5(ll,i+1)+ekont*derx(ll,3,1)
6915 gradcorr5(ll,j)=gradcorr5(ll,j)+ghalf+ekont*derx(ll,4,1)
6916 gradcorr5(ll,j1)=gradcorr5(ll,j1)+ekont*derx(ll,5,1)
6917 cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k)
6918 ghalf=0.5d0*ggg2(ll)
6920 gradcorr5(ll,k)=gradcorr5(ll,k)+ghalf+ekont*derx(ll,2,2)
6921 gradcorr5(ll,k+1)=gradcorr5(ll,k+1)+ekont*derx(ll,3,2)
6922 gradcorr5(ll,l)=gradcorr5(ll,l)+ghalf+ekont*derx(ll,4,2)
6923 gradcorr5(ll,l1)=gradcorr5(ll,l1)+ekont*derx(ll,5,2)
6928 cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*ekl*gacont_hbr(ll,jj,i)
6929 gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll)
6934 cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*eij*gacont_hbr(ll,kk,k)
6935 gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll)
6941 gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1)
6946 gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2)
6950 cd write (2,*) iii,g_corr5_loc(iii)
6954 cd write (2,*) 'ekont',ekont
6955 cd write (iout,*) 'eello5',ekont*eel5
6958 c--------------------------------------------------------------------------
6959 double precision function eello6(i,j,k,l,jj,kk)
6960 implicit real*8 (a-h,o-z)
6961 include 'DIMENSIONS'
6962 include 'DIMENSIONS.ZSCOPT'
6963 include 'COMMON.IOUNITS'
6964 include 'COMMON.CHAIN'
6965 include 'COMMON.DERIV'
6966 include 'COMMON.INTERACT'
6967 include 'COMMON.CONTACTS'
6968 include 'COMMON.TORSION'
6969 include 'COMMON.VAR'
6970 include 'COMMON.GEO'
6971 include 'COMMON.FFIELD'
6972 double precision ggg1(3),ggg2(3)
6973 cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
6978 cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
6986 cd call checkint6(i,j,k,l,jj,kk,eel6_1_num,eel6_2_num,
6987 cd & eel6_3_num,eel6_4_num,eel6_5_num,eel6_6_num)
6991 derx(lll,kkk,iii)=0.0d0
6995 cd eij=facont_hb(jj,i)
6996 cd ekl=facont_hb(kk,k)
7002 eello6_1=eello6_graph1(i,j,k,l,1,.false.)
7003 eello6_2=eello6_graph1(j,i,l,k,2,.false.)
7004 eello6_3=eello6_graph2(i,j,k,l,jj,kk,.false.)
7005 eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
7006 eello6_5=eello6_graph4(j,i,l,k,jj,kk,2,.false.)
7007 eello6_6=eello6_graph3(i,j,k,l,jj,kk,.false.)
7009 eello6_1=eello6_graph1(i,j,k,l,1,.false.)
7010 eello6_2=eello6_graph1(l,k,j,i,2,.true.)
7011 eello6_3=eello6_graph2(i,l,k,j,jj,kk,.true.)
7012 eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
7013 if (wturn6.eq.0.0d0 .or. j.ne.i+4) then
7014 eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
7018 eello6_6=eello6_graph3(i,l,k,j,jj,kk,.true.)
7020 C If turn contributions are considered, they will be handled separately.
7021 eel6=eello6_1+eello6_2+eello6_3+eello6_4+eello6_5+eello6_6
7022 cd write(iout,*) 'eello6_1',eello6_1,' eel6_1_num',16*eel6_1_num
7023 cd write(iout,*) 'eello6_2',eello6_2,' eel6_2_num',16*eel6_2_num
7024 cd write(iout,*) 'eello6_3',eello6_3,' eel6_3_num',16*eel6_3_num
7025 cd write(iout,*) 'eello6_4',eello6_4,' eel6_4_num',16*eel6_4_num
7026 cd write(iout,*) 'eello6_5',eello6_5,' eel6_5_num',16*eel6_5_num
7027 cd write(iout,*) 'eello6_6',eello6_6,' eel6_6_num',16*eel6_6_num
7030 if (j.lt.nres-1) then
7037 if (l.lt.nres-1) then
7045 ggg1(ll)=eel6*g_contij(ll,1)
7046 ggg2(ll)=eel6*g_contij(ll,2)
7047 cold ghalf=0.5d0*eel6*ekl*gacont_hbr(ll,jj,i)
7048 ghalf=0.5d0*ggg1(ll)
7050 gradcorr6(ll,i)=gradcorr6(ll,i)+ghalf+ekont*derx(ll,2,1)
7051 gradcorr6(ll,i+1)=gradcorr6(ll,i+1)+ekont*derx(ll,3,1)
7052 gradcorr6(ll,j)=gradcorr6(ll,j)+ghalf+ekont*derx(ll,4,1)
7053 gradcorr6(ll,j1)=gradcorr6(ll,j1)+ekont*derx(ll,5,1)
7054 ghalf=0.5d0*ggg2(ll)
7055 cold ghalf=0.5d0*eel6*eij*gacont_hbr(ll,kk,k)
7057 gradcorr6(ll,k)=gradcorr6(ll,k)+ghalf+ekont*derx(ll,2,2)
7058 gradcorr6(ll,k+1)=gradcorr6(ll,k+1)+ekont*derx(ll,3,2)
7059 gradcorr6(ll,l)=gradcorr6(ll,l)+ghalf+ekont*derx(ll,4,2)
7060 gradcorr6(ll,l1)=gradcorr6(ll,l1)+ekont*derx(ll,5,2)
7065 cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*ekl*gacont_hbr(ll,jj,i)
7066 gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll)
7071 cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*eij*gacont_hbr(ll,kk,k)
7072 gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll)
7078 gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1)
7083 gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2)
7087 cd write (2,*) iii,g_corr6_loc(iii)
7091 cd write (2,*) 'ekont',ekont
7092 cd write (iout,*) 'eello6',ekont*eel6
7095 c--------------------------------------------------------------------------
7096 double precision function eello6_graph1(i,j,k,l,imat,swap)
7097 implicit real*8 (a-h,o-z)
7098 include 'DIMENSIONS'
7099 include 'DIMENSIONS.ZSCOPT'
7100 include 'COMMON.IOUNITS'
7101 include 'COMMON.CHAIN'
7102 include 'COMMON.DERIV'
7103 include 'COMMON.INTERACT'
7104 include 'COMMON.CONTACTS'
7105 include 'COMMON.TORSION'
7106 include 'COMMON.VAR'
7107 include 'COMMON.GEO'
7108 double precision vv(2),vv1(2),pizda(2,2),auxmat(2,2),pizda1(2,2)
7112 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7114 C Parallel Antiparallel C
7120 C \ j|/k\| / \ |/k\|l / C
7125 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7126 itk=itortyp(itype(k))
7127 s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
7128 s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k))
7129 s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k))
7130 call transpose2(EUgC(1,1,k),auxmat(1,1))
7131 call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
7132 vv1(1)=pizda1(1,1)-pizda1(2,2)
7133 vv1(2)=pizda1(1,2)+pizda1(2,1)
7134 s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
7135 vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk)
7136 vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk)
7137 s5=scalar2(vv(1),Dtobr2(1,i))
7138 cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5
7139 eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5)
7140 if (.not. calc_grad) return
7141 if (i.gt.1) g_corr6_loc(i-1)=g_corr6_loc(i-1)
7142 & -0.5d0*ekont*(scalar2(AEAb1(1,2,imat),CUgb2der(1,i))
7143 & -scalar2(AEAb2derg(1,2,1,imat),Ug2Db1t(1,k))
7144 & +scalar2(AEAb2derg(1,2,1,imat),CUgb2(1,k))
7145 & +0.5d0*scalar2(vv1(1),Dtobr2der(1,i))
7146 & +scalar2(vv(1),Dtobr2der(1,i)))
7147 call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1))
7148 vv1(1)=pizda1(1,1)-pizda1(2,2)
7149 vv1(2)=pizda1(1,2)+pizda1(2,1)
7150 vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk)
7151 vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk)
7153 g_corr6_loc(l-1)=g_corr6_loc(l-1)
7154 & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
7155 & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
7156 & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
7157 & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
7159 g_corr6_loc(j-1)=g_corr6_loc(j-1)
7160 & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
7161 & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
7162 & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
7163 & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
7165 call transpose2(EUgCder(1,1,k),auxmat(1,1))
7166 call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
7167 vv1(1)=pizda1(1,1)-pizda1(2,2)
7168 vv1(2)=pizda1(1,2)+pizda1(2,1)
7169 if (k.gt.1) g_corr6_loc(k-1)=g_corr6_loc(k-1)
7170 & +ekont*(-0.5d0*(-scalar2(AEAb2(1,1,imat),Ug2Db1tder(1,k))
7171 & +scalar2(AEAb2(1,1,imat),CUgb2der(1,k))
7172 & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))))
7181 s1= scalar2(AEAb1derx(1,lll,kkk,iii,2,imat),CUgb2(1,i))
7182 s2=-scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),Ug2Db1t(1,k))
7183 s3= scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),CUgb2(1,k))
7184 call transpose2(EUgC(1,1,k),auxmat(1,1))
7185 call matmat2(AEAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
7187 vv1(1)=pizda1(1,1)-pizda1(2,2)
7188 vv1(2)=pizda1(1,2)+pizda1(2,1)
7189 s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
7190 vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk)
7191 & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk)
7192 vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk)
7193 & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk)
7194 s5=scalar2(vv(1),Dtobr2(1,i))
7195 derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5)
7201 c----------------------------------------------------------------------------
7202 double precision function eello6_graph2(i,j,k,l,jj,kk,swap)
7203 implicit real*8 (a-h,o-z)
7204 include 'DIMENSIONS'
7205 include 'DIMENSIONS.ZSCOPT'
7206 include 'COMMON.IOUNITS'
7207 include 'COMMON.CHAIN'
7208 include 'COMMON.DERIV'
7209 include 'COMMON.INTERACT'
7210 include 'COMMON.CONTACTS'
7211 include 'COMMON.TORSION'
7212 include 'COMMON.VAR'
7213 include 'COMMON.GEO'
7215 double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
7216 & auxvec1(2),auxvec2(2),auxmat1(2,2)
7219 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7221 C Parallel Antiparallel C
7227 C \ j|/k\| \ |/k\|l C
7232 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7233 cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
7234 C AL 7/4/01 s1 would occur in the sixth-order moment,
7235 C but not in a cluster cumulant
7237 s1=dip(1,jj,i)*dip(1,kk,k)
7239 call matvec2(ADtEA1(1,1,1),Ub2(1,k),auxvec(1))
7240 s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
7241 call matvec2(ADtEA(1,1,2),Ub2(1,l),auxvec1(1))
7242 s3=-0.5d0*scalar2(Ub2(1,j),auxvec1(1))
7243 call transpose2(EUg(1,1,k),auxmat(1,1))
7244 call matmat2(ADtEA1(1,1,1),auxmat(1,1),pizda(1,1))
7245 vv(1)=pizda(1,1)-pizda(2,2)
7246 vv(2)=pizda(1,2)+pizda(2,1)
7247 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7248 cd write (2,*) 'eello6_graph2:','s1',s1,' s2',s2,' s3',s3,' s4',s4
7250 eello6_graph2=-(s1+s2+s3+s4)
7252 eello6_graph2=-(s2+s3+s4)
7255 if (.not. calc_grad) return
7256 C Derivatives in gamma(i-1)
7259 s1=dipderg(1,jj,i)*dip(1,kk,k)
7261 s2=-0.5d0*scalar2(Ub2der(1,i),auxvec(1))
7262 call matvec2(ADtEAderg(1,1,1,2),Ub2(1,l),auxvec2(1))
7263 s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
7264 s4=-0.25d0*scalar2(vv(1),Dtobr2der(1,i))
7266 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
7268 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
7270 c g_corr6_loc(i-1)=g_corr6_loc(i-1)-s3
7272 C Derivatives in gamma(k-1)
7274 s1=dip(1,jj,i)*dipderg(1,kk,k)
7276 call matvec2(ADtEA1(1,1,1),Ub2der(1,k),auxvec2(1))
7277 s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
7278 call matvec2(ADtEAderg(1,1,2,2),Ub2(1,l),auxvec2(1))
7279 s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
7280 call transpose2(EUgder(1,1,k),auxmat1(1,1))
7281 call matmat2(ADtEA1(1,1,1),auxmat1(1,1),pizda(1,1))
7282 vv(1)=pizda(1,1)-pizda(2,2)
7283 vv(2)=pizda(1,2)+pizda(2,1)
7284 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7286 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
7288 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
7290 c g_corr6_loc(k-1)=g_corr6_loc(k-1)-s3
7291 C Derivatives in gamma(j-1) or gamma(l-1)
7294 s1=dipderg(3,jj,i)*dip(1,kk,k)
7296 call matvec2(ADtEA1derg(1,1,1,1),Ub2(1,k),auxvec2(1))
7297 s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
7298 s3=-0.5d0*scalar2(Ub2der(1,j),auxvec1(1))
7299 call matmat2(ADtEA1derg(1,1,1,1),auxmat(1,1),pizda(1,1))
7300 vv(1)=pizda(1,1)-pizda(2,2)
7301 vv(2)=pizda(1,2)+pizda(2,1)
7302 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7305 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
7307 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
7310 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s3+s4)
7311 c g_corr6_loc(j-1)=g_corr6_loc(j-1)-s3
7313 C Derivatives in gamma(l-1) or gamma(j-1)
7316 s1=dip(1,jj,i)*dipderg(3,kk,k)
7318 call matvec2(ADtEA1derg(1,1,2,1),Ub2(1,k),auxvec2(1))
7319 s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
7320 call matvec2(ADtEA(1,1,2),Ub2der(1,l),auxvec2(1))
7321 s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
7322 call matmat2(ADtEA1derg(1,1,2,1),auxmat(1,1),pizda(1,1))
7323 vv(1)=pizda(1,1)-pizda(2,2)
7324 vv(2)=pizda(1,2)+pizda(2,1)
7325 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7328 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
7330 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
7333 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s3+s4)
7334 c g_corr6_loc(l-1)=g_corr6_loc(l-1)-s3
7336 C Cartesian derivatives.
7338 write (2,*) 'In eello6_graph2'
7340 write (2,*) 'iii=',iii
7342 write (2,*) 'kkk=',kkk
7344 write (2,'(3(2f10.5),5x)')
7345 & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
7355 s1=dipderx(lll,kkk,1,jj,i)*dip(1,kk,k)
7357 s1=dip(1,jj,i)*dipderx(lll,kkk,1,kk,k)
7360 call matvec2(ADtEA1derx(1,1,lll,kkk,iii,1),Ub2(1,k),
7362 s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
7363 call matvec2(ADtEAderx(1,1,lll,kkk,iii,2),Ub2(1,l),
7365 s3=-0.5d0*scalar2(Ub2(1,j),auxvec(1))
7366 call transpose2(EUg(1,1,k),auxmat(1,1))
7367 call matmat2(ADtEA1derx(1,1,lll,kkk,iii,1),auxmat(1,1),
7369 vv(1)=pizda(1,1)-pizda(2,2)
7370 vv(2)=pizda(1,2)+pizda(2,1)
7371 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7372 cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4',s4
7374 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
7376 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
7379 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
7381 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7388 c----------------------------------------------------------------------------
7389 double precision function eello6_graph3(i,j,k,l,jj,kk,swap)
7390 implicit real*8 (a-h,o-z)
7391 include 'DIMENSIONS'
7392 include 'DIMENSIONS.ZSCOPT'
7393 include 'COMMON.IOUNITS'
7394 include 'COMMON.CHAIN'
7395 include 'COMMON.DERIV'
7396 include 'COMMON.INTERACT'
7397 include 'COMMON.CONTACTS'
7398 include 'COMMON.TORSION'
7399 include 'COMMON.VAR'
7400 include 'COMMON.GEO'
7401 double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
7403 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7405 C Parallel Antiparallel C
7411 C j|/k\| / |/k\|l / C
7416 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7418 C 4/7/01 AL Component s1 was removed, because it pertains to the respective
7419 C energy moment and not to the cluster cumulant.
7420 iti=itortyp(itype(i))
7421 if (j.lt.nres-1) then
7422 itj1=itortyp(itype(j+1))
7426 itk=itortyp(itype(k))
7427 itk1=itortyp(itype(k+1))
7428 if (l.lt.nres-1) then
7429 itl1=itortyp(itype(l+1))
7434 s1=dip(4,jj,i)*dip(4,kk,k)
7436 call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1))
7437 s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
7438 call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1))
7439 s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
7440 call transpose2(EE(1,1,itk),auxmat(1,1))
7441 call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
7442 vv(1)=pizda(1,1)+pizda(2,2)
7443 vv(2)=pizda(2,1)-pizda(1,2)
7444 s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
7445 cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4
7447 eello6_graph3=-(s1+s2+s3+s4)
7449 eello6_graph3=-(s2+s3+s4)
7452 if (.not. calc_grad) return
7453 C Derivatives in gamma(k-1)
7454 call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1))
7455 s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
7456 s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k))
7457 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4)
7458 C Derivatives in gamma(l-1)
7459 call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1))
7460 s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
7461 call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1))
7462 vv(1)=pizda(1,1)+pizda(2,2)
7463 vv(2)=pizda(2,1)-pizda(1,2)
7464 s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
7465 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
7466 C Cartesian derivatives.
7472 s1=dipderx(lll,kkk,4,jj,i)*dip(4,kk,k)
7474 s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k)
7477 call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
7479 s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
7480 call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
7482 s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
7483 call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1),
7485 vv(1)=pizda(1,1)+pizda(2,2)
7486 vv(2)=pizda(2,1)-pizda(1,2)
7487 s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
7489 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
7491 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
7494 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
7496 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7498 c derx(lll,kkk,iii)=derx(lll,kkk,iii)-s4
7504 c----------------------------------------------------------------------------
7505 double precision function eello6_graph4(i,j,k,l,jj,kk,imat,swap)
7506 implicit real*8 (a-h,o-z)
7507 include 'DIMENSIONS'
7508 include 'DIMENSIONS.ZSCOPT'
7509 include 'COMMON.IOUNITS'
7510 include 'COMMON.CHAIN'
7511 include 'COMMON.DERIV'
7512 include 'COMMON.INTERACT'
7513 include 'COMMON.CONTACTS'
7514 include 'COMMON.TORSION'
7515 include 'COMMON.VAR'
7516 include 'COMMON.GEO'
7517 include 'COMMON.FFIELD'
7518 double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
7519 & auxvec1(2),auxmat1(2,2)
7521 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7523 C Parallel Antiparallel C
7529 C \ j|/k\| \ |/k\|l C
7534 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7536 C 4/7/01 AL Component s1 was removed, because it pertains to the respective
7537 C energy moment and not to the cluster cumulant.
7538 cd write (2,*) 'eello_graph4: wturn6',wturn6
7539 iti=itortyp(itype(i))
7540 itj=itortyp(itype(j))
7541 if (j.lt.nres-1) then
7542 itj1=itortyp(itype(j+1))
7546 itk=itortyp(itype(k))
7547 if (k.lt.nres-1) then
7548 itk1=itortyp(itype(k+1))
7552 itl=itortyp(itype(l))
7553 if (l.lt.nres-1) then
7554 itl1=itortyp(itype(l+1))
7558 cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
7559 cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
7560 cd & ' itl',itl,' itl1',itl1
7563 s1=dip(3,jj,i)*dip(3,kk,k)
7565 s1=dip(2,jj,j)*dip(2,kk,l)
7568 call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1))
7569 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7571 call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1))
7572 s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
7574 call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1))
7575 s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
7577 call transpose2(EUg(1,1,k),auxmat(1,1))
7578 call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1))
7579 vv(1)=pizda(1,1)-pizda(2,2)
7580 vv(2)=pizda(2,1)+pizda(1,2)
7581 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7582 cd write (2,*) 'eello6_graph4:','s1',s1,' s2',s2,' s3',s3,' s4',s4
7584 eello6_graph4=-(s1+s2+s3+s4)
7586 eello6_graph4=-(s2+s3+s4)
7588 if (.not. calc_grad) return
7589 C Derivatives in gamma(i-1)
7593 s1=dipderg(2,jj,i)*dip(3,kk,k)
7595 s1=dipderg(4,jj,j)*dip(2,kk,l)
7598 s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1))
7600 call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1))
7601 s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
7603 call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1))
7604 s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
7606 s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i))
7607 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7608 cd write (2,*) 'turn6 derivatives'
7610 gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s1+s2+s3+s4)
7612 gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s2+s3+s4)
7616 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
7618 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
7622 C Derivatives in gamma(k-1)
7625 s1=dip(3,jj,i)*dipderg(2,kk,k)
7627 s1=dip(2,jj,j)*dipderg(4,kk,l)
7630 call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1))
7631 s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1))
7633 call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1))
7634 s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
7636 call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1))
7637 s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
7639 call transpose2(EUgder(1,1,k),auxmat1(1,1))
7640 call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1))
7641 vv(1)=pizda(1,1)-pizda(2,2)
7642 vv(2)=pizda(2,1)+pizda(1,2)
7643 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7644 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7646 gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s1+s2+s3+s4)
7648 gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s2+s3+s4)
7652 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
7654 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
7657 C Derivatives in gamma(j-1) or gamma(l-1)
7658 if (l.eq.j+1 .and. l.gt.1) then
7659 call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
7660 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7661 call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
7662 vv(1)=pizda(1,1)-pizda(2,2)
7663 vv(2)=pizda(2,1)+pizda(1,2)
7664 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7665 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
7666 else if (j.gt.1) then
7667 call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
7668 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7669 call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
7670 vv(1)=pizda(1,1)-pizda(2,2)
7671 vv(2)=pizda(2,1)+pizda(1,2)
7672 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7673 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7674 gel_loc_turn6(j-1)=gel_loc_turn6(j-1)-ekont*(s2+s4)
7676 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s4)
7679 C Cartesian derivatives.
7686 s1=dipderx(lll,kkk,3,jj,i)*dip(3,kk,k)
7688 s1=dipderx(lll,kkk,2,jj,j)*dip(2,kk,l)
7692 s1=dip(3,jj,i)*dipderx(lll,kkk,3,kk,k)
7694 s1=dip(2,jj,j)*dipderx(lll,kkk,2,kk,l)
7698 call matvec2(AECAderx(1,1,lll,kkk,iii,imat),Ub2(1,k),
7700 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7702 call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
7703 & b1(1,itj1),auxvec(1))
7704 s3=-0.5d0*scalar2(b1(1,itj),auxvec(1))
7706 call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
7707 & b1(1,itl1),auxvec(1))
7708 s3=-0.5d0*scalar2(b1(1,itl),auxvec(1))
7710 call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
7712 vv(1)=pizda(1,1)-pizda(2,2)
7713 vv(2)=pizda(2,1)+pizda(1,2)
7714 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7716 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7718 derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
7721 derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
7724 derx_turn(lll,kkk,iii)=derx_turn(lll,kkk,iii)-s3
7727 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s1+s2+s4)
7729 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s2+s4)
7731 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7735 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
7737 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
7740 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7742 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
7750 c----------------------------------------------------------------------------
7751 double precision function eello_turn6(i,jj,kk)
7752 implicit real*8 (a-h,o-z)
7753 include 'DIMENSIONS'
7754 include 'DIMENSIONS.ZSCOPT'
7755 include 'COMMON.IOUNITS'
7756 include 'COMMON.CHAIN'
7757 include 'COMMON.DERIV'
7758 include 'COMMON.INTERACT'
7759 include 'COMMON.CONTACTS'
7760 include 'COMMON.TORSION'
7761 include 'COMMON.VAR'
7762 include 'COMMON.GEO'
7763 double precision vtemp1(2),vtemp2(2),vtemp3(2),vtemp4(2),
7764 & atemp(2,2),auxmat(2,2),achuj_temp(2,2),gtemp(2,2),gvec(2),
7766 double precision vtemp1d(2),vtemp2d(2),vtemp3d(2),vtemp4d(2),
7767 & atempd(2,2),auxmatd(2,2),achuj_tempd(2,2),gtempd(2,2),gvecd(2)
7768 C 4/7/01 AL Components s1, s8, and s13 were removed, because they pertain to
7769 C the respective energy moment and not to the cluster cumulant.
7774 iti=itortyp(itype(i))
7775 itk=itortyp(itype(k))
7776 itk1=itortyp(itype(k+1))
7777 itl=itortyp(itype(l))
7778 itj=itortyp(itype(j))
7779 cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj
7780 cd write (2,*) 'i',i,' k',k,' j',j,' l',l
7781 cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
7786 cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
7788 cd call checkint_turn6(i,jj,kk,eel_turn6_num)
7792 derx_turn(lll,kkk,iii)=0.0d0
7799 eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
7801 cd write (2,*) 'eello6_5',eello6_5
7803 call transpose2(AEA(1,1,1),auxmat(1,1))
7804 call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1))
7805 ss1=scalar2(Ub2(1,i+2),b1(1,itl))
7806 s1 = (auxmat(1,1)+auxmat(2,2))*ss1
7810 call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
7811 call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1))
7812 s2 = scalar2(b1(1,itk),vtemp1(1))
7814 call transpose2(AEA(1,1,2),atemp(1,1))
7815 call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1))
7816 call matvec2(Ug2(1,1,i+2),dd(1,1,itk1),vtemp2(1))
7817 s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
7821 call matmat2(EUg(1,1,i+3),AEA(1,1,2),auxmat(1,1))
7822 call matvec2(auxmat(1,1),Ub2(1,i+4),vtemp3(1))
7823 s12 = scalar2(Ub2(1,i+2),vtemp3(1))
7825 call transpose2(a_chuj(1,1,kk,i+1),achuj_temp(1,1))
7826 call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1))
7827 call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1))
7828 call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1))
7829 ss13 = scalar2(b1(1,itk),vtemp4(1))
7830 s13 = (gtemp(1,1)+gtemp(2,2))*ss13
7834 c write (2,*) 's1,s2,s8,s12,s13',s1,s2,s8,s12,s13
7840 eel_turn6 = eello6_5 - 0.5d0*(s1+s2+s12+s8+s13)
7842 C Derivatives in gamma(i+2)
7844 call transpose2(AEA(1,1,1),auxmatd(1,1))
7845 call matmat2(EUgder(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7846 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
7847 call transpose2(AEAderg(1,1,2),atempd(1,1))
7848 call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
7849 s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
7853 call matmat2(EUg(1,1,i+3),AEAderg(1,1,2),auxmatd(1,1))
7854 call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
7855 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7861 gel_loc_turn6(i)=gel_loc_turn6(i)-0.5d0*ekont*(s1d+s8d+s12d)
7862 C Derivatives in gamma(i+3)
7864 call transpose2(AEA(1,1,1),auxmatd(1,1))
7865 call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7866 ss1d=scalar2(Ub2der(1,i+2),b1(1,itl))
7867 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d
7871 call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1))
7872 call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1))
7873 s2d = scalar2(b1(1,itk),vtemp1d(1))
7875 call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1))
7876 s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1))
7878 s12d = scalar2(Ub2der(1,i+2),vtemp3(1))
7880 call matmat2(achuj_temp(1,1),EUgder(1,1,i+2),gtempd(1,1))
7881 call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
7882 s13d = (gtempd(1,1)+gtempd(2,2))*ss13
7892 gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
7893 & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
7895 gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
7896 & -0.5d0*ekont*(s2d+s12d)
7898 C Derivatives in gamma(i+4)
7899 call matmat2(EUgder(1,1,i+3),AEA(1,1,2),auxmatd(1,1))
7900 call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
7901 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7903 call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtempd(1,1))
7904 call matmat2(gtempd(1,1),EUgder(1,1,i+3),gtempd(1,1))
7905 s13d = (gtempd(1,1)+gtempd(2,2))*ss13
7915 gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d+s13d)
7917 gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d)
7919 C Derivatives in gamma(i+5)
7921 call transpose2(AEAderg(1,1,1),auxmatd(1,1))
7922 call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7923 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
7927 call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1))
7928 call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1))
7929 s2d = scalar2(b1(1,itk),vtemp1d(1))
7931 call transpose2(AEA(1,1,2),atempd(1,1))
7932 call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1))
7933 s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
7937 call matvec2(auxmat(1,1),Ub2der(1,i+4),vtemp3d(1))
7938 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7940 call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1))
7941 ss13d = scalar2(b1(1,itk),vtemp4d(1))
7942 s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
7952 gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
7953 & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
7955 gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
7956 & -0.5d0*ekont*(s2d+s12d)
7958 C Cartesian derivatives
7963 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmatd(1,1))
7964 call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7965 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
7969 call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
7970 call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1),
7972 s2d = scalar2(b1(1,itk),vtemp1d(1))
7974 call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1))
7975 call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
7976 s8d = -(atempd(1,1)+atempd(2,2))*
7977 & scalar2(cc(1,1,itl),vtemp2(1))
7981 call matmat2(EUg(1,1,i+3),AEAderx(1,1,lll,kkk,iii,2),
7983 call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
7984 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7991 derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
7994 derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
7998 derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
7999 & - 0.5d0*(s8d+s12d)
8001 derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
8010 call transpose2(a_chuj_der(1,1,lll,kkk,kk,i+1),
8012 call matmat2(achuj_tempd(1,1),EUg(1,1,i+2),gtempd(1,1))
8013 call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
8014 s13d=(gtempd(1,1)+gtempd(2,2))*ss13
8015 derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d
8016 call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4),
8018 ss13d = scalar2(b1(1,itk),vtemp4d(1))
8019 s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
8020 derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d
8024 cd write(iout,*) 'eel6_turn6',eel_turn6,' eel_turn6_num',
8025 cd & 16*eel_turn6_num
8027 if (j.lt.nres-1) then
8034 if (l.lt.nres-1) then
8042 ggg1(ll)=eel_turn6*g_contij(ll,1)
8043 ggg2(ll)=eel_turn6*g_contij(ll,2)
8044 ghalf=0.5d0*ggg1(ll)
8046 gcorr6_turn(ll,i)=gcorr6_turn(ll,i)+ghalf
8047 & +ekont*derx_turn(ll,2,1)
8048 gcorr6_turn(ll,i+1)=gcorr6_turn(ll,i+1)+ekont*derx_turn(ll,3,1)
8049 gcorr6_turn(ll,j)=gcorr6_turn(ll,j)+ghalf
8050 & +ekont*derx_turn(ll,4,1)
8051 gcorr6_turn(ll,j1)=gcorr6_turn(ll,j1)+ekont*derx_turn(ll,5,1)
8052 ghalf=0.5d0*ggg2(ll)
8054 gcorr6_turn(ll,k)=gcorr6_turn(ll,k)+ghalf
8055 & +ekont*derx_turn(ll,2,2)
8056 gcorr6_turn(ll,k+1)=gcorr6_turn(ll,k+1)+ekont*derx_turn(ll,3,2)
8057 gcorr6_turn(ll,l)=gcorr6_turn(ll,l)+ghalf
8058 & +ekont*derx_turn(ll,4,2)
8059 gcorr6_turn(ll,l1)=gcorr6_turn(ll,l1)+ekont*derx_turn(ll,5,2)
8064 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll)
8069 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll)
8075 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1)
8080 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2)
8084 cd write (2,*) iii,g_corr6_loc(iii)
8087 eello_turn6=ekont*eel_turn6
8088 cd write (2,*) 'ekont',ekont
8089 cd write (2,*) 'eel_turn6',ekont*eel_turn6
8092 crc-------------------------------------------------
8093 SUBROUTINE MATVEC2(A1,V1,V2)
8094 implicit real*8 (a-h,o-z)
8095 include 'DIMENSIONS'
8096 DIMENSION A1(2,2),V1(2),V2(2)
8100 c 3 VI=VI+A1(I,K)*V1(K)
8104 vaux1=a1(1,1)*v1(1)+a1(1,2)*v1(2)
8105 vaux2=a1(2,1)*v1(1)+a1(2,2)*v1(2)
8110 C---------------------------------------
8111 SUBROUTINE MATMAT2(A1,A2,A3)
8112 implicit real*8 (a-h,o-z)
8113 include 'DIMENSIONS'
8114 DIMENSION A1(2,2),A2(2,2),A3(2,2)
8115 c DIMENSION AI3(2,2)
8119 c A3IJ=A3IJ+A1(I,K)*A2(K,J)
8125 ai3_11=a1(1,1)*a2(1,1)+a1(1,2)*a2(2,1)
8126 ai3_12=a1(1,1)*a2(1,2)+a1(1,2)*a2(2,2)
8127 ai3_21=a1(2,1)*a2(1,1)+a1(2,2)*a2(2,1)
8128 ai3_22=a1(2,1)*a2(1,2)+a1(2,2)*a2(2,2)
8136 c-------------------------------------------------------------------------
8137 double precision function scalar2(u,v)
8139 double precision u(2),v(2)
8142 scalar2=u(1)*v(1)+u(2)*v(2)
8146 C-----------------------------------------------------------------------------
8148 subroutine transpose2(a,at)
8150 double precision a(2,2),at(2,2)
8157 c--------------------------------------------------------------------------
8158 subroutine transpose(n,a,at)
8161 double precision a(n,n),at(n,n)
8169 C---------------------------------------------------------------------------
8170 subroutine prodmat3(a1,a2,kk,transp,prod)
8173 double precision a1(2,2),a2(2,2),a2t(2,2),kk(2,2),prod(2,2)
8175 crc double precision auxmat(2,2),prod_(2,2)
8178 crc call transpose2(kk(1,1),auxmat(1,1))
8179 crc call matmat2(a1(1,1),auxmat(1,1),auxmat(1,1))
8180 crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
8182 prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,1)
8183 & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,1)
8184 prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,2)
8185 & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,2)
8186 prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,1)
8187 & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,1)
8188 prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,2)
8189 & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,2)
8192 crc call matmat2(a1(1,1),kk(1,1),auxmat(1,1))
8193 crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
8195 prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,1)
8196 & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,1)
8197 prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,2)
8198 & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,2)
8199 prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,1)
8200 & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,1)
8201 prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,2)
8202 & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,2)
8205 c call transpose2(a2(1,1),a2t(1,1))
8208 crc print *,((prod_(i,j),i=1,2),j=1,2)
8209 crc print *,((prod(i,j),i=1,2),j=1,2)
8213 C-----------------------------------------------------------------------------
8214 double precision function scalar(u,v)
8216 double precision u(3),v(3)