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
3428 c betai=beta(i,i+1,i+2,i+3)
3430 c write (iout,*) "betai =",betai
3431 do k=1,constr_homology
3432 dih_diff(k)=pinorm(dih(k,i)-betai)
3433 c write (iout,*) "dih_diff(",k,") =",dih_diff(k)
3434 c if (dih_diff(i,k).gt.3.14159) dih_diff(i,k)=
3435 c & -(6.28318-dih_diff(i,k))
3436 c if (dih_diff(i,k).lt.-3.14159) dih_diff(i,k)=
3437 c & 6.28318+dih_diff(i,k)
3439 kat3=-0.5d0*dih_diff(k)**2*sigma_dih(k,i) ! waga_angle rmvd from Gaussian argument
3440 c kat3=-0.5d0*waga_angle*dih_diff(k)**2*sigma_dih(k,i)
3443 c write(iout,*) "kat2=", kat2, "exp(kat3)=", exp(kat3)
3446 c write (iout,*) "gdih",(gdih(k),k=1,constr_homology) ! exps
3447 c write (iout,*) "i",i," betai",betai," kat2",kat2 ! sum of exps
3449 write (iout,*) "i",i," betai",betai," kat2",kat2
3450 write (iout,*) "gdih",(gdih(k),k=1,constr_homology)
3452 if (kat2.le.1.0d-14) cycle
3453 kat=kat-dLOG(kat2/constr_homology)
3454 c write (iout,*) "kat",kat ! sum of -ln-s
3456 ccc write(iout,778)"TEST: kat2=", kat2, "DLOG(kat2)=",
3457 ccc & dLOG(kat2), "-kat=", -kat
3460 c ----------------------------------------------------------------------
3462 c ----------------------------------------------------------------------
3466 do k=1,constr_homology
3467 sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i) ! waga_angle rmvd
3468 c sgdih=-gdih(k)*dih_diff(k)*sigma_dih(k,i)*waga_angle
3469 sum_sgdih=sum_sgdih+sgdih
3471 c grad_dih3=sum_sgdih/sum_gdih
3472 grad_dih3=waga_homology(iset)*waga_angle*sum_sgdih/sum_gdih
3474 c write(iout,*)i,k,gdih,sgdih,beta(i+1,i+2,i+3,i+4),grad_dih3
3475 ccc write(iout,747) "GRAD_KAT_1", i, nphi, icg, grad_dih3,
3476 ccc & gloc(nphi+i-3,icg)
3477 gloc(i,icg)=gloc(i,icg)+grad_dih3
3479 c write(iout,*) "i",i,"icg",icg,"gloc(",i,icg,")",gloc(i,icg)
3481 ccc write(iout,747) "GRAD_KAT_2", i, nphi, icg, grad_dih3,
3482 ccc & gloc(nphi+i-3,icg)
3484 enddo ! i-loop for dih
3486 write(iout,*) "------- dih restrs end -------"
3489 c Pseudo-energy and gradient for theta angle restraints from
3490 c homology templates
3491 c FP 01/15 - inserted from econstr_local_test.F, loop structure
3495 c For constr_homology reference structures (FP)
3497 c Uconst_back_tot=0.0d0
3500 c Econstr_back legacy
3503 c do i=ithet_start,ithet_end
3506 c do i=loc_start,loc_end
3509 duscdiffx(j,i)=0.0d0
3515 c write (iout,*) "ithet_start =",ithet_start,"ithet_end =",ithet_end
3516 c write (iout,*) "waga_theta",waga_theta
3517 if (waga_theta.gt.0.0d0) then
3519 write (iout,*) "usampl",usampl
3520 write(iout,*) "------- theta restrs start -------"
3521 c do i=ithet_start,ithet_end
3522 c write (iout,*) "gloc_init(",nphi+i,icg,")",gloc(nphi+i,icg)
3525 c write (iout,*) "maxres",maxres,"nres",nres
3527 do i=ithet_start,ithet_end
3530 c ii = ifrag_back(2,i,iset)-ifrag_back(1,i,iset)
3532 c Deviation of theta angles wrt constr_homology ref structures
3534 utheta_i=0.0d0 ! argument of Gaussian for single k
3536 gutheta_i=0.0d0 ! Sum of Gaussians over constr_homology ref structures
3540 c do j=ifrag_back(1,i,iset)+2,ifrag_back(2,i,iset) ! original loop
3541 c over residues in a fragment
3542 c write (iout,*) "theta(",i,")=",theta(i)
3543 do k=1,constr_homology
3545 c dtheta_i=theta(j)-thetaref(j,iref)
3546 c dtheta_i=thetaref(k,i)-theta(i) ! original form without indexing
3547 theta_diff(k)=thetatpl(k,i)-theta(i)
3549 utheta_i=-0.5d0*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta rmvd from Gaussian argument
3550 c utheta_i=-0.5d0*waga_theta*theta_diff(k)**2*sigma_theta(k,i) ! waga_theta?
3551 gtheta(k)=dexp(utheta_i) ! + min_utheta_i?
3552 gutheta_i=gutheta_i+dexp(utheta_i) ! Sum of Gaussians (pk)
3553 c Gradient for single Gaussian restraint in subr Econstr_back
3554 c dutheta(j-2)=dutheta(j-2)+wfrag_back(1,i,iset)*dtheta_i/(ii-1)
3557 c write (iout,*) "gtheta",(gtheta(k),k=1,constr_homology) ! exps
3558 c write (iout,*) "i",i," gutheta_i",gutheta_i ! sum of exps
3562 c Gradient for multiple Gaussian restraint
3563 sum_gtheta=gutheta_i
3565 do k=1,constr_homology
3566 c New generalized expr for multiple Gaussian from Econstr_back
3567 sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i) ! waga_theta rmvd
3569 c sgtheta=-gtheta(k)*theta_diff(k)*sigma_theta(k,i)*waga_theta ! right functional form?
3570 sum_sgtheta=sum_sgtheta+sgtheta ! cum variable
3573 c Final value of gradient using same var as in Econstr_back
3574 dutheta(i-2)=sum_sgtheta/sum_gtheta*waga_theta
3575 & *waga_homology(iset)
3576 c dutheta(i)=sum_sgtheta/sum_gtheta
3578 c Uconst_back=Uconst_back+waga_theta*utheta(i) ! waga_theta added as weight
3580 Eval=Eval-dLOG(gutheta_i/constr_homology)
3581 c write (iout,*) "utheta(",i,")=",utheta(i) ! -ln of sum of exps
3582 c write (iout,*) "Uconst_back",Uconst_back ! sum of -ln-s
3583 c Uconst_back=Uconst_back+utheta(i)
3584 enddo ! (i-loop for theta)
3586 write(iout,*) "------- theta restrs end -------"
3590 c Deviation of local SC geometry
3592 c Separation of two i-loops (instructed by AL - 11/3/2014)
3594 c write (iout,*) "loc_start =",loc_start,"loc_end =",loc_end
3595 c write (iout,*) "waga_d",waga_d
3598 write(iout,*) "------- SC restrs start -------"
3599 write (iout,*) "Initial duscdiff,duscdiffx"
3600 do i=loc_start,loc_end
3601 write (iout,*) i,(duscdiff(jik,i),jik=1,3),
3602 & (duscdiffx(jik,i),jik=1,3)
3605 do i=loc_start,loc_end
3606 usc_diff_i=0.0d0 ! argument of Gaussian for single k
3608 guscdiff(i)=0.0d0 ! Sum of Gaussians over constr_homology ref structures
3612 c do j=ifrag_back(1,i,iset)+1,ifrag_back(2,i,iset)-1 ! Econstr_back legacy
3613 c write(iout,*) "xxtab, yytab, zztab"
3614 c write(iout,'(i5,3f8.2)') i,xxtab(i),yytab(i),zztab(i)
3615 do k=1,constr_homology
3617 dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
3618 c Original sign inverted for calc of gradients (s. Econstr_back)
3619 dyy=-yytpl(k,i)+yytab(i) ! ibid y
3620 dzz=-zztpl(k,i)+zztab(i) ! ibid z
3621 c write(iout,*) "dxx, dyy, dzz"
3622 c write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
3624 usc_diff_i=-0.5d0*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d rmvd from Gaussian argument
3625 c usc_diff(i)=-0.5d0*waga_d*(dxx**2+dyy**2+dzz**2)*sigma_d(k,i) ! waga_d?
3626 c uscdiffk(k)=usc_diff(i)
3627 guscdiff2(k)=dexp(usc_diff_i) ! without min_scdiff
3628 guscdiff(i)=guscdiff(i)+dexp(usc_diff_i) !Sum of Gaussians (pk)
3629 c write (iout,'(i5,6f10.5)') j,xxtab(j),yytab(j),zztab(j),
3630 c & xxref(j),yyref(j),zzref(j)
3635 c Generalized expression for multiple Gaussian acc to that for a single
3636 c Gaussian in Econstr_back as instructed by AL (FP - 03/11/2014)
3638 c Original implementation
3639 c sum_guscdiff=guscdiff(i)
3641 c sum_sguscdiff=0.0d0
3642 c do k=1,constr_homology
3643 c sguscdiff=-guscdiff2(k)*dscdiff(k)*sigma_d(k,i)*waga_d !waga_d?
3644 c sguscdiff=-guscdiff3(k)*dscdiff(k)*sigma_d(k,i)*waga_d ! w min_uscdiff
3645 c sum_sguscdiff=sum_sguscdiff+sguscdiff
3648 c Implementation of new expressions for gradient (Jan. 2015)
3650 c grad_uscdiff=sum_sguscdiff/(sum_guscdiff*dtab) !?
3652 do k=1,constr_homology
3654 c New calculation of dxx, dyy, and dzz corrected by AL (07/11), was missing and wrong
3655 c before. Now the drivatives should be correct
3657 dxx=-xxtpl(k,i)+xxtab(i) ! Diff b/w x component of ith SC vector in model and kth ref str?
3658 c Original sign inverted for calc of gradients (s. Econstr_back)
3659 dyy=-yytpl(k,i)+yytab(i) ! ibid y
3660 dzz=-zztpl(k,i)+zztab(i) ! ibid z
3662 c New implementation
3664 sum_guscdiff=guscdiff2(k)*!(dsqrt(dxx*dxx+dyy*dyy+dzz*dzz))* -> wrong!
3665 & sigma_d(k,i) ! for the grad wrt r'
3666 c sum_sguscdiff=sum_sguscdiff+sum_guscdiff
3669 c New implementation
3670 sum_guscdiff = waga_homology(iset)*waga_d*sum_guscdiff
3672 duscdiff(jik,i-1)=duscdiff(jik,i-1)+
3673 & sum_guscdiff*(dXX_C1tab(jik,i)*dxx+
3674 & dYY_C1tab(jik,i)*dyy+dZZ_C1tab(jik,i)*dzz)/guscdiff(i)
3675 duscdiff(jik,i)=duscdiff(jik,i)+
3676 & sum_guscdiff*(dXX_Ctab(jik,i)*dxx+
3677 & dYY_Ctab(jik,i)*dyy+dZZ_Ctab(jik,i)*dzz)/guscdiff(i)
3678 duscdiffx(jik,i)=duscdiffx(jik,i)+
3679 & sum_guscdiff*(dXX_XYZtab(jik,i)*dxx+
3680 & dYY_XYZtab(jik,i)*dyy+dZZ_XYZtab(jik,i)*dzz)/guscdiff(i)
3683 write(iout,*) "jik",jik,"i",i
3684 write(iout,*) "dxx, dyy, dzz"
3685 write(iout,'(2i5,3f8.2)') k,i,dxx,dyy,dzz
3686 write(iout,*) "guscdiff2(",k,")",guscdiff2(k)
3687 c write(iout,*) "sum_sguscdiff",sum_sguscdiff
3688 cc write(iout,*) "dXX_Ctab(",jik,i,")",dXX_Ctab(jik,i)
3689 c write(iout,*) "dYY_Ctab(",jik,i,")",dYY_Ctab(jik,i)
3690 c write(iout,*) "dZZ_Ctab(",jik,i,")",dZZ_Ctab(jik,i)
3691 c write(iout,*) "dXX_C1tab(",jik,i,")",dXX_C1tab(jik,i)
3692 c write(iout,*) "dYY_C1tab(",jik,i,")",dYY_C1tab(jik,i)
3693 c write(iout,*) "dZZ_C1tab(",jik,i,")",dZZ_C1tab(jik,i)
3694 c write(iout,*) "dXX_XYZtab(",jik,i,")",dXX_XYZtab(jik,i)
3695 c write(iout,*) "dYY_XYZtab(",jik,i,")",dYY_XYZtab(jik,i)
3696 c write(iout,*) "dZZ_XYZtab(",jik,i,")",dZZ_XYZtab(jik,i)
3697 c write(iout,*) "duscdiff(",jik,i-1,")",duscdiff(jik,i-1)
3698 c write(iout,*) "duscdiff(",jik,i,")",duscdiff(jik,i)
3699 c write(iout,*) "duscdiffx(",jik,i,")",duscdiffx(jik,i)
3706 c uscdiff(i)=-dLOG(guscdiff(i)/(ii-1)) ! Weighting by (ii-1) required?
3707 c usc_diff(i)=-dLOG(guscdiff(i)/constr_homology) ! + min_uscdiff ?
3709 c write (iout,*) i," uscdiff",uscdiff(i)
3711 c Put together deviations from local geometry
3713 c Uconst_back=Uconst_back+wfrag_back(1,i,iset)*utheta(i)+
3714 c & wfrag_back(3,i,iset)*uscdiff(i)
3715 Erot=Erot-dLOG(guscdiff(i)/constr_homology)
3716 c write (iout,*) "usc_diff(",i,")=",usc_diff(i) ! -ln of sum of exps
3717 c write (iout,*) "Uconst_back",Uconst_back ! cum sum of -ln-s
3718 c Uconst_back=Uconst_back+usc_diff(i)
3720 c Gradient of multiple Gaussian restraint (FP - 04/11/2014 - right?)
3722 c New implment: multiplied by sum_sguscdiff
3725 enddo ! (i-loop for dscdiff)
3730 write(iout,*) "------- SC restrs end -------"
3731 write (iout,*) "------ After SC loop in e_modeller ------"
3732 do i=loc_start,loc_end
3733 write (iout,*) "i",i," gradc",(gradc(j,i,icg),j=1,3)
3734 write (iout,*) "i",i," gradx",(gradx(j,i,icg),j=1,3)
3736 if (waga_theta.eq.1.0d0) then
3737 write (iout,*) "in e_modeller after SC restr end: dutheta"
3738 do i=ithet_start,ithet_end
3739 write (iout,*) i,dutheta(i)
3742 if (waga_d.eq.1.0d0) then
3743 write (iout,*) "e_modeller after SC loop: duscdiff/x"
3745 write (iout,*) i,(duscdiff(j,i),j=1,3)
3746 write (iout,*) i,(duscdiffx(j,i),j=1,3)
3751 c Total energy from homology restraints
3753 write (iout,*) "odleg",odleg," kat",kat
3754 write (iout,*) "odleg",odleg," kat",kat
3755 write (iout,*) "Eval",Eval," Erot",Erot
3756 write (iout,*) "waga_homology(",iset,")",waga_homology(iset)
3757 write (iout,*) "waga_dist ",waga_dist,"waga_angle ",waga_angle
3758 write (iout,*) "waga_theta ",waga_theta,"waga_d ",waga_d
3761 c Addition of energy of theta angle and SC local geom over constr_homologs ref strs
3763 c ehomology_constr=odleg+kat
3765 c For Lorentzian-type Urestr
3768 if (waga_dist.ge.0.0d0) then
3770 c For Gaussian-type Urestr
3772 c ehomology_constr=(waga_dist*odleg+waga_angle*kat+
3773 c & waga_theta*Eval+waga_d*Erot)*waga_homology(iset)
3774 ehomology_constr=waga_dist*odleg+waga_angle*kat+
3775 & waga_theta*Eval+waga_d*Erot
3776 c write (iout,*) "ehomology_constr=",ehomology_constr
3779 c For Lorentzian-type Urestr
3781 c ehomology_constr=(-waga_dist*odleg+waga_angle*kat+
3782 c & waga_theta*Eval+waga_d*Erot)*waga_homology(iset)
3783 ehomology_constr=-waga_dist*odleg+waga_angle*kat+
3784 & waga_theta*Eval+waga_d*Erot
3785 c write (iout,*) "ehomology_constr=",ehomology_constr
3788 write (iout,*) "odleg",waga_dist,odleg," kat",waga_angle,kat,
3789 & "Eval",waga_theta,eval,
3790 & "Erot",waga_d,Erot
3791 write (iout,*) "ehomology_constr",ehomology_constr
3795 748 format(a8,f12.3,a6,f12.3,a7,f12.3)
3796 747 format(a12,i4,i4,i4,f8.3,f8.3)
3797 746 format(a12,i4,i4,i4,f8.3,f8.3,f8.3)
3798 778 format(a7,1X,f10.3,1X,a4,1X,f10.3,1X,a5,1X,f10.3)
3799 779 format(i3,1X,i3,1X,i2,1X,a7,1X,f7.3,1X,a7,1X,f7.3,1X,a13,1X,
3800 & f7.3,1X,a17,1X,f9.3,1X,a10,1X,f8.3,1X,a10,1X,f8.3)
3802 c-----------------------------------------------------------------------
3803 subroutine ebond(estr)
3805 c Evaluate the energy of stretching of the CA-CA and CA-SC virtual bonds
3807 implicit real*8 (a-h,o-z)
3808 include 'DIMENSIONS'
3809 include 'DIMENSIONS.ZSCOPT'
3810 include 'DIMENSIONS.FREE'
3811 include 'COMMON.LOCAL'
3812 include 'COMMON.GEO'
3813 include 'COMMON.INTERACT'
3814 include 'COMMON.DERIV'
3815 include 'COMMON.VAR'
3816 include 'COMMON.CHAIN'
3817 include 'COMMON.IOUNITS'
3818 include 'COMMON.NAMES'
3819 include 'COMMON.FFIELD'
3820 include 'COMMON.CONTROL'
3821 double precision u(3),ud(3)
3822 logical :: lprn=.false.
3825 diff = vbld(i)-vbldp0
3826 c write (iout,*) i,vbld(i),vbldp0,diff,AKP*diff*diff
3829 gradb(j,i-1)=AKP*diff*dc(j,i-1)/vbld(i)
3834 c 09/18/07 AL: multimodal bond potential based on AM1 CA-SC PMF's included
3841 diff=vbld(i+nres)-vbldsc0(1,iti)
3843 & write (iout,*) i,iti,vbld(i+nres),vbldsc0(1,iti),diff,
3844 & AKSC(1,iti),AKSC(1,iti)*diff*diff
3845 estr=estr+0.5d0*AKSC(1,iti)*diff*diff
3847 gradbx(j,i)=AKSC(1,iti)*diff*dc(j,i+nres)/vbld(i+nres)
3851 diff=vbld(i+nres)-vbldsc0(j,iti)
3852 ud(j)=aksc(j,iti)*diff
3853 u(j)=abond0(j,iti)+0.5d0*ud(j)*diff
3867 uprod2=uprod2*u(k)*u(k)
3871 usumsqder=usumsqder+ud(j)*uprod2
3874 & write (iout,*) i,iti,vbld(i+nres),(vbldsc0(j,iti),
3875 & AKSC(j,iti),abond0(j,iti),u(j),j=1,nbi)
3876 estr=estr+uprod/usum
3878 gradbx(j,i)=usumsqder/(usum*usum)*dc(j,i+nres)/vbld(i+nres)
3886 C--------------------------------------------------------------------------
3887 subroutine ebend(etheta)
3889 C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
3890 C angles gamma and its derivatives in consecutive thetas and gammas.
3892 implicit real*8 (a-h,o-z)
3893 include 'DIMENSIONS'
3894 include 'DIMENSIONS.ZSCOPT'
3895 include 'COMMON.LOCAL'
3896 include 'COMMON.GEO'
3897 include 'COMMON.INTERACT'
3898 include 'COMMON.DERIV'
3899 include 'COMMON.VAR'
3900 include 'COMMON.CHAIN'
3901 include 'COMMON.IOUNITS'
3902 include 'COMMON.NAMES'
3903 include 'COMMON.FFIELD'
3904 common /calcthet/ term1,term2,termm,diffak,ratak,
3905 & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
3906 & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
3907 double precision y(2),z(2)
3909 time11=dexp(-2*time)
3912 c write (iout,*) "nres",nres
3913 c write (*,'(a,i2)') 'EBEND ICG=',icg
3914 c write (iout,*) ithet_start,ithet_end
3915 do i=ithet_start,ithet_end
3916 C Zero the energy function and its derivative at 0 or pi.
3917 call splinthet(theta(i),0.5d0*delta,ss,ssd)
3919 c if (i.gt.ithet_start .and.
3920 c & (itel(i-1).eq.0 .or. itel(i-2).eq.0)) goto 1215
3921 c if (i.gt.3 .and. (i.le.4 .or. itel(i-3).ne.0)) then
3929 c if (i.lt.nres .and. itel(i).ne.0) then
3941 call proc_proc(phii,icrc)
3942 if (icrc.eq.1) phii=150.0
3956 call proc_proc(phii1,icrc)
3957 if (icrc.eq.1) phii1=150.0
3969 C Calculate the "mean" value of theta from the part of the distribution
3970 C dependent on the adjacent virtual-bond-valence angles (gamma1 & gamma2).
3971 C In following comments this theta will be referred to as t_c.
3972 thet_pred_mean=0.0d0
3976 thet_pred_mean=thet_pred_mean+athetk*y(k)+bthetk*z(k)
3978 c write (iout,*) "thet_pred_mean",thet_pred_mean
3979 dthett=thet_pred_mean*ssd
3980 thet_pred_mean=thet_pred_mean*ss+a0thet(it)
3981 c write (iout,*) "thet_pred_mean",thet_pred_mean
3982 C Derivatives of the "mean" values in gamma1 and gamma2.
3983 dthetg1=(-athet(1,it)*y(2)+athet(2,it)*y(1))*ss
3984 dthetg2=(-bthet(1,it)*z(2)+bthet(2,it)*z(1))*ss
3985 if (theta(i).gt.pi-delta) then
3986 call theteng(pi-delta,thet_pred_mean,theta0(it),f0,fprim0,
3988 call mixder(pi-delta,thet_pred_mean,theta0(it),fprim_tc0)
3989 call theteng(pi,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
3990 call spline1(theta(i),pi-delta,delta,f0,f1,fprim0,ethetai,
3992 call spline2(theta(i),pi-delta,delta,E_tc0,E_tc1,fprim_tc0,
3994 else if (theta(i).lt.delta) then
3995 call theteng(delta,thet_pred_mean,theta0(it),f0,fprim0,E_tc0)
3996 call theteng(0.0d0,thet_pred_mean,theta0(it),f1,fprim1,E_tc1)
3997 call spline1(theta(i),delta,-delta,f0,f1,fprim0,ethetai,
3999 call mixder(delta,thet_pred_mean,theta0(it),fprim_tc0)
4000 call spline2(theta(i),delta,-delta,E_tc0,E_tc1,fprim_tc0,
4003 call theteng(theta(i),thet_pred_mean,theta0(it),ethetai,
4006 etheta=etheta+ethetai
4007 c write (iout,'(2i3,3f8.3,f10.5)') i,it,rad2deg*theta(i),
4008 c & rad2deg*phii,rad2deg*phii1,ethetai
4009 if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*E_tc*dthetg1
4010 if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*E_tc*dthetg2
4011 gloc(nphi+i-2,icg)=wang*(E_theta+E_tc*dthett)
4014 C Ufff.... We've done all this!!!
4017 C---------------------------------------------------------------------------
4018 subroutine theteng(thetai,thet_pred_mean,theta0i,ethetai,E_theta,
4020 implicit real*8 (a-h,o-z)
4021 include 'DIMENSIONS'
4022 include 'COMMON.LOCAL'
4023 include 'COMMON.IOUNITS'
4024 common /calcthet/ term1,term2,termm,diffak,ratak,
4025 & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
4026 & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
4027 C Calculate the contributions to both Gaussian lobes.
4028 C 6/6/97 - Deform the Gaussians using the factor of 1/(1+time)
4029 C The "polynomial part" of the "standard deviation" of this part of
4033 sig=sig*thet_pred_mean+polthet(j,it)
4035 C Derivative of the "interior part" of the "standard deviation of the"
4036 C gamma-dependent Gaussian lobe in t_c.
4037 sigtc=3*polthet(3,it)
4039 sigtc=sigtc*thet_pred_mean+j*polthet(j,it)
4042 C Set the parameters of both Gaussian lobes of the distribution.
4043 C "Standard deviation" of the gamma-dependent Gaussian lobe (sigtc)
4044 fac=sig*sig+sigc0(it)
4047 C Following variable (sigsqtc) is -(1/2)d[sigma(t_c)**(-2))]/dt_c
4048 sigsqtc=-4.0D0*sigcsq*sigtc
4049 c print *,i,sig,sigtc,sigsqtc
4050 C Following variable (sigtc) is d[sigma(t_c)]/dt_c
4051 sigtc=-sigtc/(fac*fac)
4052 C Following variable is sigma(t_c)**(-2)
4053 sigcsq=sigcsq*sigcsq
4055 sig0inv=1.0D0/sig0i**2
4056 delthec=thetai-thet_pred_mean
4057 delthe0=thetai-theta0i
4058 term1=-0.5D0*sigcsq*delthec*delthec
4059 term2=-0.5D0*sig0inv*delthe0*delthe0
4060 C Following fuzzy logic is to avoid underflows in dexp and subsequent INFs and
4061 C NaNs in taking the logarithm. We extract the largest exponent which is added
4062 C to the energy (this being the log of the distribution) at the end of energy
4063 C term evaluation for this virtual-bond angle.
4064 if (term1.gt.term2) then
4066 term2=dexp(term2-termm)
4070 term1=dexp(term1-termm)
4073 C The ratio between the gamma-independent and gamma-dependent lobes of
4074 C the distribution is a Gaussian function of thet_pred_mean too.
4075 diffak=gthet(2,it)-thet_pred_mean
4076 ratak=diffak/gthet(3,it)**2
4077 ak=dexp(gthet(1,it)-0.5D0*diffak*ratak)
4078 C Let's differentiate it in thet_pred_mean NOW.
4080 C Now put together the distribution terms to make complete distribution.
4081 termexp=term1+ak*term2
4082 termpre=sigc+ak*sig0i
4083 C Contribution of the bending energy from this theta is just the -log of
4084 C the sum of the contributions from the two lobes and the pre-exponential
4085 C factor. Simple enough, isn't it?
4086 ethetai=(-dlog(termexp)-termm+dlog(termpre))
4087 C NOW the derivatives!!!
4088 C 6/6/97 Take into account the deformation.
4089 E_theta=(delthec*sigcsq*term1
4090 & +ak*delthe0*sig0inv*term2)/termexp
4091 E_tc=((sigtc+aktc*sig0i)/termpre
4092 & -((delthec*sigcsq+delthec*delthec*sigsqtc)*term1+
4093 & aktc*term2)/termexp)
4096 c-----------------------------------------------------------------------------
4097 subroutine mixder(thetai,thet_pred_mean,theta0i,E_tc_t)
4098 implicit real*8 (a-h,o-z)
4099 include 'DIMENSIONS'
4100 include 'COMMON.LOCAL'
4101 include 'COMMON.IOUNITS'
4102 common /calcthet/ term1,term2,termm,diffak,ratak,
4103 & ak,aktc,termpre,termexp,sigc,sig0i,time11,time12,sigcsq,
4104 & delthe0,sig0inv,sigtc,sigsqtc,delthec,it
4105 delthec=thetai-thet_pred_mean
4106 delthe0=thetai-theta0i
4107 C "Thank you" to MAPLE (probably spared one day of hand-differentiation).
4108 t3 = thetai-thet_pred_mean
4112 t14 = t12+t6*sigsqtc
4114 t21 = thetai-theta0i
4120 E_tc_t = -((sigcsq+2.D0*t3*sigsqtc)*t9-t14*sigcsq*t3*t16*t9
4121 & -aktc*sig0inv*t27)/t32+(t14*t9+aktc*t26)/t40
4122 & *(-t12*t9-ak*sig0inv*t27)
4126 C--------------------------------------------------------------------------
4127 subroutine ebend(etheta)
4129 C Evaluate the virtual-bond-angle energy given the virtual-bond dihedral
4130 C angles gamma and its derivatives in consecutive thetas and gammas.
4131 C ab initio-derived potentials from
4132 c Kozlowska et al., J. Phys.: Condens. Matter 19 (2007) 285203
4134 implicit real*8 (a-h,o-z)
4135 include 'DIMENSIONS'
4136 include 'DIMENSIONS.ZSCOPT'
4137 include 'DIMENSIONS.FREE'
4138 include 'COMMON.LOCAL'
4139 include 'COMMON.GEO'
4140 include 'COMMON.INTERACT'
4141 include 'COMMON.DERIV'
4142 include 'COMMON.VAR'
4143 include 'COMMON.CHAIN'
4144 include 'COMMON.IOUNITS'
4145 include 'COMMON.NAMES'
4146 include 'COMMON.FFIELD'
4147 include 'COMMON.CONTROL'
4148 double precision coskt(mmaxtheterm),sinkt(mmaxtheterm),
4149 & cosph1(maxsingle),sinph1(maxsingle),cosph2(maxsingle),
4150 & sinph2(maxsingle),cosph1ph2(maxdouble,maxdouble),
4151 & sinph1ph2(maxdouble,maxdouble)
4152 logical lprn /.false./, lprn1 /.false./
4154 c write (iout,*) "ithetyp",(ithetyp(i),i=1,ntyp1)
4155 do i=ithet_start,ithet_end
4156 if ((itype(i-1).eq.ntyp1).or.(itype(i-2).eq.ntyp1).or.
4157 & (itype(i).eq.ntyp1)) cycle
4161 theti2=0.5d0*theta(i)
4162 ityp2=ithetyp(itype(i-1))
4164 coskt(k)=dcos(k*theti2)
4165 sinkt(k)=dsin(k*theti2)
4167 if (i.gt.3 .and. itype(max0(i-3,1)).ne.ntyp1) then
4170 if (phii.ne.phii) phii=150.0
4174 ityp1=ithetyp(itype(i-2))
4176 cosph1(k)=dcos(k*phii)
4177 sinph1(k)=dsin(k*phii)
4181 ityp1=ithetyp(itype(i-2))
4187 if (i.lt.nres .and. itype(i+1).ne.ntyp1) then
4190 if (phii1.ne.phii1) phii1=150.0
4195 ityp3=ithetyp(itype(i))
4197 cosph2(k)=dcos(k*phii1)
4198 sinph2(k)=dsin(k*phii1)
4203 ityp3=ithetyp(itype(i))
4209 c write (iout,*) "i",i," ityp1",itype(i-2),ityp1,
4210 c & " ityp2",itype(i-1),ityp2," ityp3",itype(i),ityp3
4212 ethetai=aa0thet(ityp1,ityp2,ityp3)
4215 ccl=cosph1(l)*cosph2(k-l)
4216 ssl=sinph1(l)*sinph2(k-l)
4217 scl=sinph1(l)*cosph2(k-l)
4218 csl=cosph1(l)*sinph2(k-l)
4219 cosph1ph2(l,k)=ccl-ssl
4220 cosph1ph2(k,l)=ccl+ssl
4221 sinph1ph2(l,k)=scl+csl
4222 sinph1ph2(k,l)=scl-csl
4226 write (iout,*) "i",i," ityp1",ityp1," ityp2",ityp2,
4227 & " ityp3",ityp3," theti2",theti2," phii",phii," phii1",phii1
4228 write (iout,*) "coskt and sinkt"
4230 write (iout,*) k,coskt(k),sinkt(k)
4234 ethetai=ethetai+aathet(k,ityp1,ityp2,ityp3)*sinkt(k)
4235 dethetai=dethetai+0.5d0*k*aathet(k,ityp1,ityp2,ityp3)
4238 & write (iout,*) "k",k," aathet",aathet(k,ityp1,ityp2,ityp3),
4239 & " ethetai",ethetai
4242 write (iout,*) "cosph and sinph"
4244 write (iout,*) k,cosph1(k),sinph1(k),cosph2(k),sinph2(k)
4246 write (iout,*) "cosph1ph2 and sinph2ph2"
4249 write (iout,*) l,k,cosph1ph2(l,k),cosph1ph2(k,l),
4250 & sinph1ph2(l,k),sinph1ph2(k,l)
4253 write(iout,*) "ethetai",ethetai
4257 aux=bbthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)
4258 & +ccthet(k,m,ityp1,ityp2,ityp3)*sinph1(k)
4259 & +ddthet(k,m,ityp1,ityp2,ityp3)*cosph2(k)
4260 & +eethet(k,m,ityp1,ityp2,ityp3)*sinph2(k)
4261 ethetai=ethetai+sinkt(m)*aux
4262 dethetai=dethetai+0.5d0*m*aux*coskt(m)
4263 dephii=dephii+k*sinkt(m)*(
4264 & ccthet(k,m,ityp1,ityp2,ityp3)*cosph1(k)-
4265 & bbthet(k,m,ityp1,ityp2,ityp3)*sinph1(k))
4266 dephii1=dephii1+k*sinkt(m)*(
4267 & eethet(k,m,ityp1,ityp2,ityp3)*cosph2(k)-
4268 & ddthet(k,m,ityp1,ityp2,ityp3)*sinph2(k))
4270 & write (iout,*) "m",m," k",k," bbthet",
4271 & bbthet(k,m,ityp1,ityp2,ityp3)," ccthet",
4272 & ccthet(k,m,ityp1,ityp2,ityp3)," ddthet",
4273 & ddthet(k,m,ityp1,ityp2,ityp3)," eethet",
4274 & eethet(k,m,ityp1,ityp2,ityp3)," ethetai",ethetai
4278 & write(iout,*) "ethetai",ethetai
4282 aux=ffthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)+
4283 & ffthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l)+
4284 & ggthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
4285 & ggthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)
4286 ethetai=ethetai+sinkt(m)*aux
4287 dethetai=dethetai+0.5d0*m*coskt(m)*aux
4288 dephii=dephii+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))
4293 dephii1=dephii1+(k-l)*sinkt(m)*(
4294 & -ffthet(l,k,m,ityp1,ityp2,ityp3)*sinph1ph2(l,k)+
4295 & ffthet(k,l,m,ityp1,ityp2,ityp3)*sinph1ph2(k,l)+
4296 & ggthet(l,k,m,ityp1,ityp2,ityp3)*cosph1ph2(l,k)-
4297 & ggthet(k,l,m,ityp1,ityp2,ityp3)*cosph1ph2(k,l))
4299 write (iout,*) "m",m," k",k," l",l," ffthet",
4300 & ffthet(l,k,m,ityp1,ityp2,ityp3),
4301 & ffthet(k,l,m,ityp1,ityp2,ityp3)," ggthet",
4302 & ggthet(l,k,m,ityp1,ityp2,ityp3),
4303 & ggthet(k,l,m,ityp1,ityp2,ityp3)," ethetai",ethetai
4304 write (iout,*) cosph1ph2(l,k)*sinkt(m),
4305 & cosph1ph2(k,l)*sinkt(m),
4306 & sinph1ph2(l,k)*sinkt(m),sinph1ph2(k,l)*sinkt(m)
4313 if (lprn1) write (iout,'(a4,i2,3f8.1,9h ethetai ,f10.5)')
4314 & 'ebe',i,theta(i)*rad2deg,phii*rad2deg,
4315 & phii1*rad2deg,ethetai
4317 etheta=etheta+ethetai
4319 if (i.gt.3) gloc(i-3,icg)=gloc(i-3,icg)+wang*dephii
4320 if (i.lt.nres) gloc(i-2,icg)=gloc(i-2,icg)+wang*dephii1
4321 gloc(nphi+i-2,icg)=wang*dethetai
4327 c-----------------------------------------------------------------------------
4328 subroutine esc(escloc)
4329 C Calculate the local energy of a side chain and its derivatives in the
4330 C corresponding virtual-bond valence angles THETA and the spherical angles
4332 implicit real*8 (a-h,o-z)
4333 include 'DIMENSIONS'
4334 include 'DIMENSIONS.ZSCOPT'
4335 include 'COMMON.GEO'
4336 include 'COMMON.LOCAL'
4337 include 'COMMON.VAR'
4338 include 'COMMON.INTERACT'
4339 include 'COMMON.DERIV'
4340 include 'COMMON.CHAIN'
4341 include 'COMMON.IOUNITS'
4342 include 'COMMON.NAMES'
4343 include 'COMMON.FFIELD'
4344 double precision x(3),dersc(3),xemp(3),dersc0(3),dersc1(3),
4345 & ddersc0(3),ddummy(3),xtemp(3),temp(3)
4346 common /sccalc/ time11,time12,time112,theti,it,nlobit
4349 c write (iout,'(a)') 'ESC'
4350 do i=loc_start,loc_end
4352 if (it.eq.10) goto 1
4354 c print *,'i=',i,' it=',it,' nlobit=',nlobit
4355 c write (iout,*) 'i=',i,' ssa=',ssa,' ssad=',ssad
4356 theti=theta(i+1)-pipol
4360 c write (iout,*) "i",i," x",x(1),x(2),x(3)
4362 if (x(2).gt.pi-delta) then
4366 call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
4368 call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
4369 call spline1(x(2),pi-delta,delta,escloci0,escloci1,dersc0(2),
4371 call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
4372 & ddersc0(1),dersc(1))
4373 call spline2(x(2),pi-delta,delta,dersc0(3),dersc1(3),
4374 & ddersc0(3),dersc(3))
4376 call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
4378 call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
4379 call spline1(x(2),pi-delta,delta,esclocbi0,esclocbi1,
4380 & dersc0(2),esclocbi,dersc02)
4381 call spline2(x(2),pi-delta,delta,dersc0(1),dersc1(1),
4383 call splinthet(x(2),0.5d0*delta,ss,ssd)
4388 dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
4390 dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
4391 c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
4393 escloci=ss*escloci+(1.0d0-ss)*esclocbi
4395 c write (iout,*) escloci
4396 else if (x(2).lt.delta) then
4400 call enesc(xtemp,escloci0,dersc0,ddersc0,.true.)
4402 call enesc(xtemp,escloci1,dersc1,ddummy,.false.)
4403 call spline1(x(2),delta,-delta,escloci0,escloci1,dersc0(2),
4405 call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
4406 & ddersc0(1),dersc(1))
4407 call spline2(x(2),delta,-delta,dersc0(3),dersc1(3),
4408 & ddersc0(3),dersc(3))
4410 call enesc_bound(xtemp,esclocbi0,dersc0,dersc12,.true.)
4412 call enesc_bound(xtemp,esclocbi1,dersc1,chuju,.false.)
4413 call spline1(x(2),delta,-delta,esclocbi0,esclocbi1,
4414 & dersc0(2),esclocbi,dersc02)
4415 call spline2(x(2),delta,-delta,dersc0(1),dersc1(1),
4420 call splinthet(x(2),0.5d0*delta,ss,ssd)
4422 dersc(k)=ss*dersc(k)+(1.0d0-ss)*dersc0(k)
4424 dersc(2)=dersc(2)+ssd*(escloci-esclocbi)
4425 c write (iout,*) 'i=',i,x(2)*rad2deg,escloci0,escloci,
4427 escloci=ss*escloci+(1.0d0-ss)*esclocbi
4428 c write (iout,*) escloci
4430 call enesc(x,escloci,dersc,ddummy,.false.)
4433 escloc=escloc+escloci
4434 c write (iout,*) 'i=',i,' escloci=',escloci,' dersc=',dersc
4436 gloc(nphi+i-1,icg)=gloc(nphi+i-1,icg)+
4438 gloc(ialph(i,1),icg)=wscloc*dersc(2)
4439 gloc(ialph(i,1)+nside,icg)=wscloc*dersc(3)
4444 C---------------------------------------------------------------------------
4445 subroutine enesc(x,escloci,dersc,ddersc,mixed)
4446 implicit real*8 (a-h,o-z)
4447 include 'DIMENSIONS'
4448 include 'COMMON.GEO'
4449 include 'COMMON.LOCAL'
4450 include 'COMMON.IOUNITS'
4451 common /sccalc/ time11,time12,time112,theti,it,nlobit
4452 double precision x(3),z(3),Ax(3,maxlob,-1:1),dersc(3),ddersc(3)
4453 double precision contr(maxlob,-1:1)
4455 c write (iout,*) 'it=',it,' nlobit=',nlobit
4459 if (mixed) ddersc(j)=0.0d0
4463 C Because of periodicity of the dependence of the SC energy in omega we have
4464 C to add up the contributions from x(3)-2*pi, x(3), and x(3+2*pi).
4465 C To avoid underflows, first compute & store the exponents.
4473 z(k)=x(k)-censc(k,j,it)
4478 Axk=Axk+gaussc(l,k,j,it)*z(l)
4484 expfac=expfac+Ax(k,j,iii)*z(k)
4492 C As in the case of ebend, we want to avoid underflows in exponentiation and
4493 C subsequent NaNs and INFs in energy calculation.
4494 C Find the largest exponent
4498 if (emin.gt.contr(j,iii)) emin=contr(j,iii)
4502 cd print *,'it=',it,' emin=',emin
4504 C Compute the contribution to SC energy and derivatives
4508 expfac=dexp(bsc(j,it)-0.5D0*contr(j,iii)+emin)
4509 cd print *,'j=',j,' expfac=',expfac
4510 escloc_i=escloc_i+expfac
4512 dersc(k)=dersc(k)+Ax(k,j,iii)*expfac
4516 ddersc(k)=ddersc(k)+(-Ax(2,j,iii)*Ax(k,j,iii)
4517 & +gaussc(k,2,j,it))*expfac
4524 dersc(1)=dersc(1)/cos(theti)**2
4525 ddersc(1)=ddersc(1)/cos(theti)**2
4528 escloci=-(dlog(escloc_i)-emin)
4530 dersc(j)=dersc(j)/escloc_i
4534 ddersc(j)=(ddersc(j)/escloc_i+dersc(2)*dersc(j))
4539 C------------------------------------------------------------------------------
4540 subroutine enesc_bound(x,escloci,dersc,dersc12,mixed)
4541 implicit real*8 (a-h,o-z)
4542 include 'DIMENSIONS'
4543 include 'COMMON.GEO'
4544 include 'COMMON.LOCAL'
4545 include 'COMMON.IOUNITS'
4546 common /sccalc/ time11,time12,time112,theti,it,nlobit
4547 double precision x(3),z(3),Ax(3,maxlob),dersc(3)
4548 double precision contr(maxlob)
4559 z(k)=x(k)-censc(k,j,it)
4565 Axk=Axk+gaussc(l,k,j,it)*z(l)
4571 expfac=expfac+Ax(k,j)*z(k)
4576 C As in the case of ebend, we want to avoid underflows in exponentiation and
4577 C subsequent NaNs and INFs in energy calculation.
4578 C Find the largest exponent
4581 if (emin.gt.contr(j)) emin=contr(j)
4585 C Compute the contribution to SC energy and derivatives
4589 expfac=dexp(bsc(j,it)-0.5D0*contr(j)+emin)
4590 escloc_i=escloc_i+expfac
4592 dersc(k)=dersc(k)+Ax(k,j)*expfac
4594 if (mixed) dersc12=dersc12+(-Ax(2,j)*Ax(1,j)
4595 & +gaussc(1,2,j,it))*expfac
4599 dersc(1)=dersc(1)/cos(theti)**2
4600 dersc12=dersc12/cos(theti)**2
4601 escloci=-(dlog(escloc_i)-emin)
4603 dersc(j)=dersc(j)/escloc_i
4605 if (mixed) dersc12=(dersc12/escloc_i+dersc(2)*dersc(1))
4609 c----------------------------------------------------------------------------------
4610 subroutine esc(escloc)
4611 C Calculate the local energy of a side chain and its derivatives in the
4612 C corresponding virtual-bond valence angles THETA and the spherical angles
4613 C ALPHA and OMEGA derived from AM1 all-atom calculations.
4614 C added by Urszula Kozlowska. 07/11/2007
4616 implicit real*8 (a-h,o-z)
4617 include 'DIMENSIONS'
4618 include 'DIMENSIONS.ZSCOPT'
4619 include 'DIMENSIONS.FREE'
4620 include 'COMMON.GEO'
4621 include 'COMMON.LOCAL'
4622 include 'COMMON.VAR'
4623 include 'COMMON.SCROT'
4624 include 'COMMON.INTERACT'
4625 include 'COMMON.DERIV'
4626 include 'COMMON.CHAIN'
4627 include 'COMMON.IOUNITS'
4628 include 'COMMON.NAMES'
4629 include 'COMMON.FFIELD'
4630 include 'COMMON.CONTROL'
4631 include 'COMMON.VECTORS'
4632 double precision x_prime(3),y_prime(3),z_prime(3)
4633 & , sumene,dsc_i,dp2_i,x(65),
4634 & xx,yy,zz,sumene1,sumene2,sumene3,sumene4,s1,s1_6,s2,s2_6,
4635 & de_dxx,de_dyy,de_dzz,de_dt
4636 double precision s1_t,s1_6_t,s2_t,s2_6_t
4638 & dXX_Ci1(3),dYY_Ci1(3),dZZ_Ci1(3),dXX_Ci(3),
4639 & dYY_Ci(3),dZZ_Ci(3),dXX_XYZ(3),dYY_XYZ(3),dZZ_XYZ(3),
4640 & dt_dCi(3),dt_dCi1(3)
4641 common /sccalc/ time11,time12,time112,theti,it,nlobit
4644 do i=loc_start,loc_end
4645 costtab(i+1) =dcos(theta(i+1))
4646 sinttab(i+1) =dsqrt(1-costtab(i+1)*costtab(i+1))
4647 cost2tab(i+1)=dsqrt(0.5d0*(1.0d0+costtab(i+1)))
4648 sint2tab(i+1)=dsqrt(0.5d0*(1.0d0-costtab(i+1)))
4649 cosfac2=0.5d0/(1.0d0+costtab(i+1))
4650 cosfac=dsqrt(cosfac2)
4651 sinfac2=0.5d0/(1.0d0-costtab(i+1))
4652 sinfac=dsqrt(sinfac2)
4654 if (it.eq.10) goto 1
4656 C Compute the axes of tghe local cartesian coordinates system; store in
4657 c x_prime, y_prime and z_prime
4664 C write(2,*) "dc_norm", dc_norm(1,i+nres),dc_norm(2,i+nres),
4665 C & dc_norm(3,i+nres)
4667 x_prime(j) = (dc_norm(j,i) - dc_norm(j,i-1))*cosfac
4668 y_prime(j) = (dc_norm(j,i) + dc_norm(j,i-1))*sinfac
4671 z_prime(j) = -uz(j,i-1)
4674 c write (2,*) "x_prime",(x_prime(j),j=1,3)
4675 c write (2,*) "y_prime",(y_prime(j),j=1,3)
4676 c write (2,*) "z_prime",(z_prime(j),j=1,3)
4677 c write (2,*) "xx",scalar(x_prime(1),x_prime(1)),
4678 c & " xy",scalar(x_prime(1),y_prime(1)),
4679 c & " xz",scalar(x_prime(1),z_prime(1)),
4680 c & " yy",scalar(y_prime(1),y_prime(1)),
4681 c & " yz",scalar(y_prime(1),z_prime(1)),
4682 c & " zz",scalar(z_prime(1),z_prime(1))
4684 C Transform the unit vector of the ith side-chain centroid, dC_norm(*,i),
4685 C to local coordinate system. Store in xx, yy, zz.
4691 xx = xx + x_prime(j)*dc_norm(j,i+nres)
4692 yy = yy + y_prime(j)*dc_norm(j,i+nres)
4693 zz = zz + z_prime(j)*dc_norm(j,i+nres)
4700 C Compute the energy of the ith side cbain
4702 c write (2,*) "xx",xx," yy",yy," zz",zz
4705 x(j) = sc_parmin(j,it)
4708 Cc diagnostics - remove later
4710 yy1 = dsin(alph(2))*dcos(omeg(2))
4711 zz1 = -dsin(alph(2))*dsin(omeg(2))
4712 write(2,'(3f8.1,3f9.3,1x,3f9.3)')
4713 & alph(2)*rad2deg,omeg(2)*rad2deg,theta(3)*rad2deg,xx,yy,zz,
4715 C," --- ", xx_w,yy_w,zz_w
4718 sumene1= x(1)+ x(2)*xx+ x(3)*yy+ x(4)*zz+ x(5)*xx**2
4719 & + x(6)*yy**2+ x(7)*zz**2+ x(8)*xx*zz+ x(9)*xx*yy
4721 sumene2= x(11) + x(12)*xx + x(13)*yy + x(14)*zz + x(15)*xx**2
4722 & + x(16)*yy**2 + x(17)*zz**2 + x(18)*xx*zz + x(19)*xx*yy
4724 sumene3= x(21) +x(22)*xx +x(23)*yy +x(24)*zz +x(25)*xx**2
4725 & +x(26)*yy**2 +x(27)*zz**2 +x(28)*xx*zz +x(29)*xx*yy
4726 & +x(30)*yy*zz +x(31)*xx**3 +x(32)*yy**3 +x(33)*zz**3
4727 & +x(34)*(xx**2)*yy +x(35)*(xx**2)*zz +x(36)*(yy**2)*xx
4728 & +x(37)*(yy**2)*zz +x(38)*(zz**2)*xx +x(39)*(zz**2)*yy
4730 sumene4= x(41) +x(42)*xx +x(43)*yy +x(44)*zz +x(45)*xx**2
4731 & +x(46)*yy**2 +x(47)*zz**2 +x(48)*xx*zz +x(49)*xx*yy
4732 & +x(50)*yy*zz +x(51)*xx**3 +x(52)*yy**3 +x(53)*zz**3
4733 & +x(54)*(xx**2)*yy +x(55)*(xx**2)*zz +x(56)*(yy**2)*xx
4734 & +x(57)*(yy**2)*zz +x(58)*(zz**2)*xx +x(59)*(zz**2)*yy
4736 dsc_i = 0.743d0+x(61)
4738 dscp1=dsqrt(dsc_i**2+dp2_i**2-2*dsc_i*dp2_i
4739 & *(xx*cost2tab(i+1)+yy*sint2tab(i+1)))
4740 dscp2=dsqrt(dsc_i**2+dp2_i**2-2*dsc_i*dp2_i
4741 & *(xx*cost2tab(i+1)-yy*sint2tab(i+1)))
4742 s1=(1+x(63))/(0.1d0 + dscp1)
4743 s1_6=(1+x(64))/(0.1d0 + dscp1**6)
4744 s2=(1+x(65))/(0.1d0 + dscp2)
4745 s2_6=(1+x(65))/(0.1d0 + dscp2**6)
4746 sumene = ( sumene3*sint2tab(i+1) + sumene1)*(s1+s1_6)
4747 & + (sumene4*cost2tab(i+1) +sumene2)*(s2+s2_6)
4748 c write(2,'(i2," sumene",7f9.3)') i,sumene1,sumene2,sumene3,
4750 c & dscp1,dscp2,sumene
4751 c sumene = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4752 escloc = escloc + sumene
4753 c write (2,*) "escloc",escloc
4754 if (.not. calc_grad) goto 1
4758 C This section to check the numerical derivatives of the energy of ith side
4759 C chain in xx, yy, zz, and theta. Use the -DDEBUG compiler option or insert
4760 C #define DEBUG in the code to turn it on.
4762 write (2,*) "sumene =",sumene
4766 write (2,*) xx,yy,zz
4767 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4768 de_dxx_num=(sumenep-sumene)/aincr
4770 write (2,*) "xx+ sumene from enesc=",sumenep
4773 write (2,*) xx,yy,zz
4774 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4775 de_dyy_num=(sumenep-sumene)/aincr
4777 write (2,*) "yy+ sumene from enesc=",sumenep
4780 write (2,*) xx,yy,zz
4781 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4782 de_dzz_num=(sumenep-sumene)/aincr
4784 write (2,*) "zz+ sumene from enesc=",sumenep
4785 costsave=cost2tab(i+1)
4786 sintsave=sint2tab(i+1)
4787 cost2tab(i+1)=dcos(0.5d0*(theta(i+1)+aincr))
4788 sint2tab(i+1)=dsin(0.5d0*(theta(i+1)+aincr))
4789 sumenep = enesc(x,xx,yy,zz,cost2tab(i+1),sint2tab(i+1))
4790 de_dt_num=(sumenep-sumene)/aincr
4791 write (2,*) " t+ sumene from enesc=",sumenep
4792 cost2tab(i+1)=costsave
4793 sint2tab(i+1)=sintsave
4794 C End of diagnostics section.
4797 C Compute the gradient of esc
4799 pom_s1=(1.0d0+x(63))/(0.1d0 + dscp1)**2
4800 pom_s16=6*(1.0d0+x(64))/(0.1d0 + dscp1**6)**2
4801 pom_s2=(1.0d0+x(65))/(0.1d0 + dscp2)**2
4802 pom_s26=6*(1.0d0+x(65))/(0.1d0 + dscp2**6)**2
4803 pom_dx=dsc_i*dp2_i*cost2tab(i+1)
4804 pom_dy=dsc_i*dp2_i*sint2tab(i+1)
4805 pom_dt1=-0.5d0*dsc_i*dp2_i*(xx*sint2tab(i+1)-yy*cost2tab(i+1))
4806 pom_dt2=-0.5d0*dsc_i*dp2_i*(xx*sint2tab(i+1)+yy*cost2tab(i+1))
4807 pom1=(sumene3*sint2tab(i+1)+sumene1)
4808 & *(pom_s1/dscp1+pom_s16*dscp1**4)
4809 pom2=(sumene4*cost2tab(i+1)+sumene2)
4810 & *(pom_s2/dscp2+pom_s26*dscp2**4)
4811 sumene1x=x(2)+2*x(5)*xx+x(8)*zz+ x(9)*yy
4812 sumene3x=x(22)+2*x(25)*xx+x(28)*zz+x(29)*yy+3*x(31)*xx**2
4813 & +2*x(34)*xx*yy +2*x(35)*xx*zz +x(36)*(yy**2) +x(38)*(zz**2)
4815 sumene2x=x(12)+2*x(15)*xx+x(18)*zz+ x(19)*yy
4816 sumene4x=x(42)+2*x(45)*xx +x(48)*zz +x(49)*yy +3*x(51)*xx**2
4817 & +2*x(54)*xx*yy+2*x(55)*xx*zz+x(56)*(yy**2)+x(58)*(zz**2)
4819 de_dxx =(sumene1x+sumene3x*sint2tab(i+1))*(s1+s1_6)
4820 & +(sumene2x+sumene4x*cost2tab(i+1))*(s2+s2_6)
4821 & +(pom1+pom2)*pom_dx
4823 write(2,*), "de_dxx = ", de_dxx,de_dxx_num
4826 sumene1y=x(3) + 2*x(6)*yy + x(9)*xx + x(10)*zz
4827 sumene3y=x(23) +2*x(26)*yy +x(29)*xx +x(30)*zz +3*x(32)*yy**2
4828 & +x(34)*(xx**2) +2*x(36)*yy*xx +2*x(37)*yy*zz +x(39)*(zz**2)
4830 sumene2y=x(13) + 2*x(16)*yy + x(19)*xx + x(20)*zz
4831 sumene4y=x(43)+2*x(46)*yy+x(49)*xx +x(50)*zz
4832 & +3*x(52)*yy**2+x(54)*xx**2+2*x(56)*yy*xx +2*x(57)*yy*zz
4833 & +x(59)*zz**2 +x(60)*xx*zz
4834 de_dyy =(sumene1y+sumene3y*sint2tab(i+1))*(s1+s1_6)
4835 & +(sumene2y+sumene4y*cost2tab(i+1))*(s2+s2_6)
4836 & +(pom1-pom2)*pom_dy
4838 write(2,*), "de_dyy = ", de_dyy,de_dyy_num
4841 de_dzz =(x(24) +2*x(27)*zz +x(28)*xx +x(30)*yy
4842 & +3*x(33)*zz**2 +x(35)*xx**2 +x(37)*yy**2 +2*x(38)*zz*xx
4843 & +2*x(39)*zz*yy +x(40)*xx*yy)*sint2tab(i+1)*(s1+s1_6)
4844 & +(x(4) + 2*x(7)*zz+ x(8)*xx + x(10)*yy)*(s1+s1_6)
4845 & +(x(44)+2*x(47)*zz +x(48)*xx +x(50)*yy +3*x(53)*zz**2
4846 & +x(55)*xx**2 +x(57)*(yy**2)+2*x(58)*zz*xx +2*x(59)*zz*yy
4847 & +x(60)*xx*yy)*cost2tab(i+1)*(s2+s2_6)
4848 & + ( x(14) + 2*x(17)*zz+ x(18)*xx + x(20)*yy)*(s2+s2_6)
4850 write(2,*), "de_dzz = ", de_dzz,de_dzz_num
4853 de_dt = 0.5d0*sumene3*cost2tab(i+1)*(s1+s1_6)
4854 & -0.5d0*sumene4*sint2tab(i+1)*(s2+s2_6)
4855 & +pom1*pom_dt1+pom2*pom_dt2
4857 write(2,*), "de_dt = ", de_dt,de_dt_num
4861 cossc=scalar(dc_norm(1,i),dc_norm(1,i+nres))
4862 cossc1=scalar(dc_norm(1,i-1),dc_norm(1,i+nres))
4863 cosfac2xx=cosfac2*xx
4864 sinfac2yy=sinfac2*yy
4866 dt_dCi(k) = -(dc_norm(k,i-1)+costtab(i+1)*dc_norm(k,i))*
4868 dt_dCi1(k)= -(dc_norm(k,i)+costtab(i+1)*dc_norm(k,i-1))*
4870 pom=(dC_norm(k,i+nres)-cossc*dC_norm(k,i))*vbld_inv(i+1)
4871 pom1=(dC_norm(k,i+nres)-cossc1*dC_norm(k,i-1))*vbld_inv(i)
4872 c write (iout,*) "i",i," k",k," pom",pom," pom1",pom1,
4873 c & " dt_dCi",dt_dCi(k)," dt_dCi1",dt_dCi1(k)
4874 c write (iout,*) "dC_norm",(dC_norm(j,i),j=1,3),
4875 c & (dC_norm(j,i-1),j=1,3)," vbld_inv",vbld_inv(i+1),vbld_inv(i)
4876 dXX_Ci(k)=pom*cosfac-dt_dCi(k)*cosfac2xx
4877 dXX_Ci1(k)=-pom1*cosfac-dt_dCi1(k)*cosfac2xx
4878 dYY_Ci(k)=pom*sinfac+dt_dCi(k)*sinfac2yy
4879 dYY_Ci1(k)=pom1*sinfac+dt_dCi1(k)*sinfac2yy
4883 dZZ_Ci(k)=dZZ_Ci(k)-uzgrad(j,k,2,i-1)*dC_norm(j,i+nres)
4884 dZZ_Ci1(k)=dZZ_Ci1(k)-uzgrad(j,k,1,i-1)*dC_norm(j,i+nres)
4887 dXX_XYZ(k)=vbld_inv(i+nres)*(x_prime(k)-xx*dC_norm(k,i+nres))
4888 dYY_XYZ(k)=vbld_inv(i+nres)*(y_prime(k)-yy*dC_norm(k,i+nres))
4889 dZZ_XYZ(k)=vbld_inv(i+nres)*(z_prime(k)-zz*dC_norm(k,i+nres))
4891 dt_dCi(k) = -dt_dCi(k)/sinttab(i+1)
4892 dt_dCi1(k)= -dt_dCi1(k)/sinttab(i+1)
4896 dXX_Ctab(k,i)=dXX_Ci(k)
4897 dXX_C1tab(k,i)=dXX_Ci1(k)
4898 dYY_Ctab(k,i)=dYY_Ci(k)
4899 dYY_C1tab(k,i)=dYY_Ci1(k)
4900 dZZ_Ctab(k,i)=dZZ_Ci(k)
4901 dZZ_C1tab(k,i)=dZZ_Ci1(k)
4902 dXX_XYZtab(k,i)=dXX_XYZ(k)
4903 dYY_XYZtab(k,i)=dYY_XYZ(k)
4904 dZZ_XYZtab(k,i)=dZZ_XYZ(k)
4908 c write (iout,*) "k",k," dxx_ci1",dxx_ci1(k)," dyy_ci1",
4909 c & dyy_ci1(k)," dzz_ci1",dzz_ci1(k)
4910 c write (iout,*) "k",k," dxx_ci",dxx_ci(k)," dyy_ci",
4911 c & dyy_ci(k)," dzz_ci",dzz_ci(k)
4912 c write (iout,*) "k",k," dt_dci",dt_dci(k)," dt_dci",
4914 c write (iout,*) "k",k," dxx_XYZ",dxx_XYZ(k)," dyy_XYZ",
4915 c & dyy_XYZ(k)," dzz_XYZ",dzz_XYZ(k)
4916 gscloc(k,i-1)=gscloc(k,i-1)+de_dxx*dxx_ci1(k)
4917 & +de_dyy*dyy_ci1(k)+de_dzz*dzz_ci1(k)+de_dt*dt_dCi1(k)
4918 gscloc(k,i)=gscloc(k,i)+de_dxx*dxx_Ci(k)
4919 & +de_dyy*dyy_Ci(k)+de_dzz*dzz_Ci(k)+de_dt*dt_dCi(k)
4920 gsclocx(k,i)= de_dxx*dxx_XYZ(k)
4921 & +de_dyy*dyy_XYZ(k)+de_dzz*dzz_XYZ(k)
4923 c write(iout,*) "ENERGY GRAD = ", (gscloc(k,i-1),k=1,3),
4924 c & (gscloc(k,i),k=1,3),(gsclocx(k,i),k=1,3)
4926 C to check gradient call subroutine check_grad
4933 c------------------------------------------------------------------------------
4934 subroutine gcont(rij,r0ij,eps0ij,delta,fcont,fprimcont)
4936 C This procedure calculates two-body contact function g(rij) and its derivative:
4939 C g(rij) = esp0ij*(-0.9375*x+0.625*x**3-0.1875*x**5) ! -1 =< x =< 1
4942 C where x=(rij-r0ij)/delta
4944 C rij - interbody distance, r0ij - contact distance, eps0ij - contact energy
4947 double precision rij,r0ij,eps0ij,fcont,fprimcont
4948 double precision x,x2,x4,delta
4952 if (x.lt.-1.0D0) then
4955 else if (x.le.1.0D0) then
4958 fcont=eps0ij*(x*(-0.9375D0+0.6250D0*x2-0.1875D0*x4)+0.5D0)
4959 fprimcont=eps0ij * (-0.9375D0+1.8750D0*x2-0.9375D0*x4)/delta
4966 c------------------------------------------------------------------------------
4967 subroutine splinthet(theti,delta,ss,ssder)
4968 implicit real*8 (a-h,o-z)
4969 include 'DIMENSIONS'
4970 include 'DIMENSIONS.ZSCOPT'
4971 include 'COMMON.VAR'
4972 include 'COMMON.GEO'
4975 if (theti.gt.pipol) then
4976 call gcont(theti,thetup,1.0d0,delta,ss,ssder)
4978 call gcont(-theti,-thetlow,1.0d0,delta,ss,ssder)
4983 c------------------------------------------------------------------------------
4984 subroutine spline1(x,x0,delta,f0,f1,fprim0,f,fprim)
4986 double precision x,x0,delta,f0,f1,fprim0,f,fprim
4987 double precision ksi,ksi2,ksi3,a1,a2,a3
4988 a1=fprim0*delta/(f1-f0)
4994 f=f0+(f1-f0)*ksi*(a1+ksi*(a2+a3*ksi))
4995 fprim=(f1-f0)/delta*(a1+ksi*(2*a2+3*ksi*a3))
4998 c------------------------------------------------------------------------------
4999 subroutine spline2(x,x0,delta,f0x,f1x,fprim0x,fx)
5001 double precision x,x0,delta,f0x,f1x,fprim0x,fx
5002 double precision ksi,ksi2,ksi3,a1,a2,a3
5007 a2=3*(f1x-f0x)-2*fprim0x*delta
5008 a3=fprim0x*delta-2*(f1x-f0x)
5009 fx=f0x+a1*ksi+a2*ksi2+a3*ksi3
5012 C-----------------------------------------------------------------------------
5014 C-----------------------------------------------------------------------------
5015 subroutine etor(etors,edihcnstr,fact)
5016 implicit real*8 (a-h,o-z)
5017 include 'DIMENSIONS'
5018 include 'DIMENSIONS.ZSCOPT'
5019 include 'COMMON.VAR'
5020 include 'COMMON.GEO'
5021 include 'COMMON.LOCAL'
5022 include 'COMMON.TORSION'
5023 include 'COMMON.INTERACT'
5024 include 'COMMON.DERIV'
5025 include 'COMMON.CHAIN'
5026 include 'COMMON.NAMES'
5027 include 'COMMON.IOUNITS'
5028 include 'COMMON.FFIELD'
5029 include 'COMMON.TORCNSTR'
5031 C Set lprn=.true. for debugging
5035 do i=iphi_start,iphi_end
5036 itori=itortyp(itype(i-2))
5037 itori1=itortyp(itype(i-1))
5040 C Proline-Proline pair is a special case...
5041 if (itori.eq.3 .and. itori1.eq.3) then
5042 if (phii.gt.-dwapi3) then
5044 fac=1.0D0/(1.0D0-cosphi)
5045 etorsi=v1(1,3,3)*fac
5046 etorsi=etorsi+etorsi
5047 etors=etors+etorsi-v1(1,3,3)
5048 gloci=gloci-3*fac*etorsi*dsin(3*phii)
5051 v1ij=v1(j+1,itori,itori1)
5052 v2ij=v2(j+1,itori,itori1)
5055 etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
5056 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5060 v1ij=v1(j,itori,itori1)
5061 v2ij=v2(j,itori,itori1)
5064 etors=etors+v1ij*cosphi+v2ij*sinphi+dabs(v1ij)+dabs(v2ij)
5065 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5069 & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
5070 & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
5071 & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
5072 gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
5073 c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
5075 ! 6/20/98 - dihedral angle constraints
5078 itori=idih_constr(i)
5081 if (difi.gt.drange(i)) then
5083 edihcnstr=edihcnstr+0.25d0*ftors*difi**4
5084 gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
5085 else if (difi.lt.-drange(i)) then
5087 edihcnstr=edihcnstr+0.25d0*ftors*difi**4
5088 gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
5090 ! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
5091 ! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
5093 ! write (iout,*) 'edihcnstr',edihcnstr
5096 c------------------------------------------------------------------------------
5098 subroutine etor(etors,edihcnstr,fact)
5099 implicit real*8 (a-h,o-z)
5100 include 'DIMENSIONS'
5101 include 'DIMENSIONS.ZSCOPT'
5102 include 'COMMON.VAR'
5103 include 'COMMON.GEO'
5104 include 'COMMON.LOCAL'
5105 include 'COMMON.TORSION'
5106 include 'COMMON.INTERACT'
5107 include 'COMMON.DERIV'
5108 include 'COMMON.CHAIN'
5109 include 'COMMON.NAMES'
5110 include 'COMMON.IOUNITS'
5111 include 'COMMON.FFIELD'
5112 include 'COMMON.TORCNSTR'
5114 C Set lprn=.true. for debugging
5118 do i=iphi_start,iphi_end
5119 if (itel(i-2).eq.0 .or. itel(i-1).eq.0) goto 1215
5120 itori=itortyp(itype(i-2))
5121 itori1=itortyp(itype(i-1))
5124 C Regular cosine and sine terms
5125 do j=1,nterm(itori,itori1)
5126 v1ij=v1(j,itori,itori1)
5127 v2ij=v2(j,itori,itori1)
5130 etors=etors+v1ij*cosphi+v2ij*sinphi
5131 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5135 C E = SUM ----------------------------------- - v1
5136 C [v2 cos(phi/2)+v3 sin(phi/2)]^2 + 1
5138 cosphi=dcos(0.5d0*phii)
5139 sinphi=dsin(0.5d0*phii)
5140 do j=1,nlor(itori,itori1)
5141 vl1ij=vlor1(j,itori,itori1)
5142 vl2ij=vlor2(j,itori,itori1)
5143 vl3ij=vlor3(j,itori,itori1)
5144 pom=vl2ij*cosphi+vl3ij*sinphi
5145 pom1=1.0d0/(pom*pom+1.0d0)
5146 etors=etors+vl1ij*pom1
5148 gloci=gloci+vl1ij*(vl3ij*cosphi-vl2ij*sinphi)*pom
5150 C Subtract the constant term
5151 etors=etors-v0(itori,itori1)
5153 & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
5154 & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
5155 & (v1(j,itori,itori1),j=1,6),(v2(j,itori,itori1),j=1,6)
5156 gloc(i-3,icg)=gloc(i-3,icg)+wtor*fact*gloci
5157 c write (iout,*) 'i=',i,' gloc=',gloc(i-3,icg)
5160 ! 6/20/98 - dihedral angle constraints
5163 itori=idih_constr(i)
5165 difi=pinorm(phii-phi0(i))
5167 if (difi.gt.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
5172 else if (difi.lt.-drange(i)) then
5174 edihcnstr=edihcnstr+0.25d0*ftors*difi**4
5175 gloc(itori-3,icg)=gloc(itori-3,icg)+ftors*difi**3
5176 edihi=0.25d0*ftors*difi**4
5180 c write (iout,'(2i5,4f10.5,e15.5)') i,itori,phii,phi0(i),difi,
5182 ! write (iout,'(2i5,2f8.3,2e14.5)') i,itori,rad2deg*phii,
5183 ! & rad2deg*difi,0.25d0*ftors*difi**4,gloc(itori-3,icg)
5185 ! write (iout,*) 'edihcnstr',edihcnstr
5188 c----------------------------------------------------------------------------
5189 subroutine etor_d(etors_d,fact2)
5190 C 6/23/01 Compute double torsional energy
5191 implicit real*8 (a-h,o-z)
5192 include 'DIMENSIONS'
5193 include 'DIMENSIONS.ZSCOPT'
5194 include 'COMMON.VAR'
5195 include 'COMMON.GEO'
5196 include 'COMMON.LOCAL'
5197 include 'COMMON.TORSION'
5198 include 'COMMON.INTERACT'
5199 include 'COMMON.DERIV'
5200 include 'COMMON.CHAIN'
5201 include 'COMMON.NAMES'
5202 include 'COMMON.IOUNITS'
5203 include 'COMMON.FFIELD'
5204 include 'COMMON.TORCNSTR'
5206 C Set lprn=.true. for debugging
5210 do i=iphi_start,iphi_end-1
5211 if (itel(i-2).eq.0 .or. itel(i-1).eq.0 .or. itel(i).eq.0)
5213 itori=itortyp(itype(i-2))
5214 itori1=itortyp(itype(i-1))
5215 itori2=itortyp(itype(i))
5220 C Regular cosine and sine terms
5221 do j=1,ntermd_1(itori,itori1,itori2)
5222 v1cij=v1c(1,j,itori,itori1,itori2)
5223 v1sij=v1s(1,j,itori,itori1,itori2)
5224 v2cij=v1c(2,j,itori,itori1,itori2)
5225 v2sij=v1s(2,j,itori,itori1,itori2)
5226 cosphi1=dcos(j*phii)
5227 sinphi1=dsin(j*phii)
5228 cosphi2=dcos(j*phii1)
5229 sinphi2=dsin(j*phii1)
5230 etors_d=etors_d+v1cij*cosphi1+v1sij*sinphi1+
5231 & v2cij*cosphi2+v2sij*sinphi2
5232 gloci1=gloci1+j*(v1sij*cosphi1-v1cij*sinphi1)
5233 gloci2=gloci2+j*(v2sij*cosphi2-v2cij*sinphi2)
5235 do k=2,ntermd_2(itori,itori1,itori2)
5237 v1cdij = v2c(k,l,itori,itori1,itori2)
5238 v2cdij = v2c(l,k,itori,itori1,itori2)
5239 v1sdij = v2s(k,l,itori,itori1,itori2)
5240 v2sdij = v2s(l,k,itori,itori1,itori2)
5241 cosphi1p2=dcos(l*phii+(k-l)*phii1)
5242 cosphi1m2=dcos(l*phii-(k-l)*phii1)
5243 sinphi1p2=dsin(l*phii+(k-l)*phii1)
5244 sinphi1m2=dsin(l*phii-(k-l)*phii1)
5245 etors_d=etors_d+v1cdij*cosphi1p2+v2cdij*cosphi1m2+
5246 & v1sdij*sinphi1p2+v2sdij*sinphi1m2
5247 gloci1=gloci1+l*(v1sdij*cosphi1p2+v2sdij*cosphi1m2
5248 & -v1cdij*sinphi1p2-v2cdij*sinphi1m2)
5249 gloci2=gloci2+(k-l)*(v1sdij*cosphi1p2-v2sdij*cosphi1m2
5250 & -v1cdij*sinphi1p2+v2cdij*sinphi1m2)
5253 gloc(i-3,icg)=gloc(i-3,icg)+wtor_d*fact2*gloci1
5254 gloc(i-2,icg)=gloc(i-2,icg)+wtor_d*fact2*gloci2
5260 c------------------------------------------------------------------------------
5261 subroutine eback_sc_corr(esccor)
5262 c 7/21/2007 Correlations between the backbone-local and side-chain-local
5263 c conformational states; temporarily implemented as differences
5264 c between UNRES torsional potentials (dependent on three types of
5265 c residues) and the torsional potentials dependent on all 20 types
5266 c of residues computed from AM1 energy surfaces of terminally-blocked
5267 c amino-acid residues.
5268 implicit real*8 (a-h,o-z)
5269 include 'DIMENSIONS'
5270 include 'DIMENSIONS.ZSCOPT'
5271 include 'DIMENSIONS.FREE'
5272 include 'COMMON.VAR'
5273 include 'COMMON.GEO'
5274 include 'COMMON.LOCAL'
5275 include 'COMMON.TORSION'
5276 include 'COMMON.SCCOR'
5277 include 'COMMON.INTERACT'
5278 include 'COMMON.DERIV'
5279 include 'COMMON.CHAIN'
5280 include 'COMMON.NAMES'
5281 include 'COMMON.IOUNITS'
5282 include 'COMMON.FFIELD'
5283 include 'COMMON.CONTROL'
5285 C Set lprn=.true. for debugging
5288 c write (iout,*) "EBACK_SC_COR",itau_start,itau_end,nterm_sccor
5290 do i=itau_start,itau_end
5292 if ((itype(i-2).eq.ntyp1).or.(itype(i-1).eq.ntyp1)) cycle
5293 isccori=isccortyp(itype(i-2))
5294 isccori1=isccortyp(itype(i-1))
5296 cccc Added 9 May 2012
5297 cc Tauangle is torsional engle depending on the value of first digit
5298 c(see comment below)
5299 cc Omicron is flat angle depending on the value of first digit
5300 c(see comment below)
5303 do intertyp=1,3 !intertyp
5304 cc Added 09 May 2012 (Adasko)
5305 cc Intertyp means interaction type of backbone mainchain correlation:
5306 c 1 = SC...Ca...Ca...Ca
5307 c 2 = Ca...Ca...Ca...SC
5308 c 3 = SC...Ca...Ca...SCi
5310 if (((intertyp.eq.3).and.((itype(i-2).eq.10).or.
5311 & (itype(i-1).eq.10).or.(itype(i-2).eq.21).or.
5312 & (itype(i-1).eq.21)))
5313 & .or. ((intertyp.eq.1).and.((itype(i-2).eq.10)
5314 & .or.(itype(i-2).eq.21)))
5315 & .or.((intertyp.eq.2).and.((itype(i-1).eq.10).or.
5316 & (itype(i-1).eq.21)))) cycle
5317 if ((intertyp.eq.2).and.(i.eq.4).and.(itype(1).eq.21)) cycle
5318 if ((intertyp.eq.1).and.(i.eq.nres).and.(itype(nres).eq.21))
5320 do j=1,nterm_sccor(isccori,isccori1)
5321 v1ij=v1sccor(j,intertyp,isccori,isccori1)
5322 v2ij=v2sccor(j,intertyp,isccori,isccori1)
5323 cosphi=dcos(j*tauangle(intertyp,i))
5324 sinphi=dsin(j*tauangle(intertyp,i))
5325 esccor=esccor+v1ij*cosphi+v2ij*sinphi
5327 esccor_ii=esccor_ii+v1ij*cosphi+v2ij*sinphi
5329 gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
5331 gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
5332 c write (iout,*) "WTF",intertyp,i,itype(i),v1ij*cosphi+v2ij*sinphi
5333 c &gloc_sc(intertyp,i-3,icg)
5335 & write (iout,'(2(a3,2x,i3,2x),2i3,6f8.3/26x,6f8.3/)')
5336 & restyp(itype(i-2)),i-2,restyp(itype(i-1)),i-1,itori,itori1,
5337 & (v1sccor(j,intertyp,itori,itori1),j=1,6)
5338 & ,(v2sccor(j,intertyp,itori,itori1),j=1,6)
5339 gsccor_loc(i-3)=gsccor_loc(i-3)+gloci
5342 write (iout,*) "i",i,(tauangle(j,i),j=1,3),esccor_ii
5346 c write (iout,*) "W@T@F", gloc_sc(1,i,icg),gloc(i,icg)
5350 c------------------------------------------------------------------------------
5351 subroutine multibody(ecorr)
5352 C This subroutine calculates multi-body contributions to energy following
5353 C the idea of Skolnick et al. If side chains I and J make a contact and
5354 C at the same time side chains I+1 and J+1 make a contact, an extra
5355 C contribution equal to sqrt(eps(i,j)*eps(i+1,j+1)) is added.
5356 implicit real*8 (a-h,o-z)
5357 include 'DIMENSIONS'
5358 include 'COMMON.IOUNITS'
5359 include 'COMMON.DERIV'
5360 include 'COMMON.INTERACT'
5361 include 'COMMON.CONTACTS'
5362 double precision gx(3),gx1(3)
5365 C Set lprn=.true. for debugging
5369 write (iout,'(a)') 'Contact function values:'
5371 write (iout,'(i2,20(1x,i2,f10.5))')
5372 & i,(jcont(j,i),facont(j,i),j=1,num_cont(i))
5387 num_conti=num_cont(i)
5388 num_conti1=num_cont(i1)
5393 if (j1.eq.j+ishift .or. j1.eq.j-ishift) then
5394 cd write(iout,*)'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5395 cd & ' ishift=',ishift
5396 C Contacts I--J and I+ISHIFT--J+-ISHIFT1 occur simultaneously.
5397 C The system gains extra energy.
5398 ecorr=ecorr+esccorr(i,j,i1,j1,jj,kk)
5399 endif ! j1==j+-ishift
5408 c------------------------------------------------------------------------------
5409 double precision function esccorr(i,j,k,l,jj,kk)
5410 implicit real*8 (a-h,o-z)
5411 include 'DIMENSIONS'
5412 include 'COMMON.IOUNITS'
5413 include 'COMMON.DERIV'
5414 include 'COMMON.INTERACT'
5415 include 'COMMON.CONTACTS'
5416 double precision gx(3),gx1(3)
5421 cd write (iout,'(4i5,3f10.5)') i,j,k,l,eij,ekl,-eij*ekl
5422 C Calculate the multi-body contribution to energy.
5423 C Calculate multi-body contributions to the gradient.
5424 cd write (iout,'(2(2i3,3f10.5))')i,j,(gacont(m,jj,i),m=1,3),
5425 cd & k,l,(gacont(m,kk,k),m=1,3)
5427 gx(m) =ekl*gacont(m,jj,i)
5428 gx1(m)=eij*gacont(m,kk,k)
5429 gradxorr(m,i)=gradxorr(m,i)-gx(m)
5430 gradxorr(m,j)=gradxorr(m,j)+gx(m)
5431 gradxorr(m,k)=gradxorr(m,k)-gx1(m)
5432 gradxorr(m,l)=gradxorr(m,l)+gx1(m)
5436 gradcorr(ll,m)=gradcorr(ll,m)+gx(ll)
5441 gradcorr(ll,m)=gradcorr(ll,m)+gx1(ll)
5447 c------------------------------------------------------------------------------
5449 subroutine pack_buffer(dimen1,dimen2,atom,indx,buffer)
5450 implicit real*8 (a-h,o-z)
5451 include 'DIMENSIONS'
5452 integer dimen1,dimen2,atom,indx
5453 double precision buffer(dimen1,dimen2)
5454 double precision zapas
5455 common /contacts_hb/ zapas(3,20,maxres,7),
5456 & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
5457 & num_cont_hb(maxres),jcont_hb(20,maxres)
5458 num_kont=num_cont_hb(atom)
5462 buffer(i,indx+(k-1)*3+j)=zapas(j,i,atom,k)
5465 buffer(i,indx+22)=facont_hb(i,atom)
5466 buffer(i,indx+23)=ees0p(i,atom)
5467 buffer(i,indx+24)=ees0m(i,atom)
5468 buffer(i,indx+25)=dfloat(jcont_hb(i,atom))
5470 buffer(1,indx+26)=dfloat(num_kont)
5473 c------------------------------------------------------------------------------
5474 subroutine unpack_buffer(dimen1,dimen2,atom,indx,buffer)
5475 implicit real*8 (a-h,o-z)
5476 include 'DIMENSIONS'
5477 integer dimen1,dimen2,atom,indx
5478 double precision buffer(dimen1,dimen2)
5479 double precision zapas
5480 common /contacts_hb/ zapas(3,20,maxres,7),
5481 & facont_hb(20,maxres),ees0p(20,maxres),ees0m(20,maxres),
5482 & num_cont_hb(maxres),jcont_hb(20,maxres)
5483 num_kont=buffer(1,indx+26)
5484 num_kont_old=num_cont_hb(atom)
5485 num_cont_hb(atom)=num_kont+num_kont_old
5490 zapas(j,ii,atom,k)=buffer(i,indx+(k-1)*3+j)
5493 facont_hb(ii,atom)=buffer(i,indx+22)
5494 ees0p(ii,atom)=buffer(i,indx+23)
5495 ees0m(ii,atom)=buffer(i,indx+24)
5496 jcont_hb(ii,atom)=buffer(i,indx+25)
5500 c------------------------------------------------------------------------------
5502 subroutine multibody_hb(ecorr,ecorr5,ecorr6,n_corr,n_corr1)
5503 C This subroutine calculates multi-body contributions to hydrogen-bonding
5504 implicit real*8 (a-h,o-z)
5505 include 'DIMENSIONS'
5506 include 'DIMENSIONS.ZSCOPT'
5507 include 'COMMON.IOUNITS'
5509 include 'COMMON.INFO'
5511 include 'COMMON.FFIELD'
5512 include 'COMMON.DERIV'
5513 include 'COMMON.INTERACT'
5514 include 'COMMON.CONTACTS'
5516 parameter (max_cont=maxconts)
5517 parameter (max_dim=2*(8*3+2))
5518 parameter (msglen1=max_cont*max_dim*4)
5519 parameter (msglen2=2*msglen1)
5520 integer source,CorrelType,CorrelID,Error
5521 double precision buffer(max_cont,max_dim)
5523 double precision gx(3),gx1(3)
5526 C Set lprn=.true. for debugging
5531 if (fgProcs.le.1) goto 30
5533 write (iout,'(a)') 'Contact function values:'
5535 write (iout,'(2i3,50(1x,i2,f5.2))')
5536 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5537 & j=1,num_cont_hb(i))
5540 C Caution! Following code assumes that electrostatic interactions concerning
5541 C a given atom are split among at most two processors!
5551 cd write (iout,*) 'MyRank',MyRank,' mm',mm
5554 cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
5555 if (MyRank.gt.0) then
5556 C Send correlation contributions to the preceding processor
5558 nn=num_cont_hb(iatel_s)
5559 call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
5560 cd write (iout,*) 'The BUFFER array:'
5562 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
5564 if (ielstart(iatel_s).gt.iatel_s+ispp) then
5566 call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
5567 C Clear the contacts of the atom passed to the neighboring processor
5568 nn=num_cont_hb(iatel_s+1)
5570 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
5572 num_cont_hb(iatel_s)=0
5574 cd write (iout,*) 'Processor ',MyID,MyRank,
5575 cd & ' is sending correlation contribution to processor',MyID-1,
5576 cd & ' msglen=',msglen
5577 cd write (*,*) 'Processor ',MyID,MyRank,
5578 cd & ' is sending correlation contribution to processor',MyID-1,
5579 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5580 call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
5581 cd write (iout,*) 'Processor ',MyID,
5582 cd & ' has sent correlation contribution to processor',MyID-1,
5583 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5584 cd write (*,*) 'Processor ',MyID,
5585 cd & ' has sent correlation contribution to processor',MyID-1,
5586 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5588 endif ! (MyRank.gt.0)
5592 cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
5593 if (MyRank.lt.fgProcs-1) then
5594 C Receive correlation contributions from the next processor
5596 if (ielend(iatel_e).lt.nct-1) msglen=msglen2
5597 cd write (iout,*) 'Processor',MyID,
5598 cd & ' is receiving correlation contribution from processor',MyID+1,
5599 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5600 cd write (*,*) 'Processor',MyID,
5601 cd & ' is receiving correlation contribution from processor',MyID+1,
5602 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5604 do while (nbytes.le.0)
5605 call mp_probe(MyID+1,CorrelType,nbytes)
5607 cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
5608 call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
5609 cd write (iout,*) 'Processor',MyID,
5610 cd & ' has received correlation contribution from processor',MyID+1,
5611 cd & ' msglen=',msglen,' nbytes=',nbytes
5612 cd write (iout,*) 'The received BUFFER array:'
5614 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
5616 if (msglen.eq.msglen1) then
5617 call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
5618 else if (msglen.eq.msglen2) then
5619 call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
5620 call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
5623 & 'ERROR!!!! message length changed while processing correlations.'
5625 & 'ERROR!!!! message length changed while processing correlations.'
5626 call mp_stopall(Error)
5627 endif ! msglen.eq.msglen1
5628 endif ! MyRank.lt.fgProcs-1
5635 write (iout,'(a)') 'Contact function values:'
5637 write (iout,'(2i3,50(1x,i2,f5.2))')
5638 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5639 & j=1,num_cont_hb(i))
5643 C Remove the loop below after debugging !!!
5650 C Calculate the local-electrostatic correlation terms
5651 do i=iatel_s,iatel_e+1
5653 num_conti=num_cont_hb(i)
5654 num_conti1=num_cont_hb(i+1)
5659 c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5660 c & ' jj=',jj,' kk=',kk
5661 if (j1.eq.j+1 .or. j1.eq.j-1) then
5662 C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
5663 C The system gains extra energy.
5664 ecorr=ecorr+ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
5666 write (iout,*) "ecorr",i,j,i+1,j1,
5667 & ehbcorr(i,j,i+1,j1,jj,kk,0.72D0,0.32D0)
5670 else if (j1.eq.j) then
5671 C Contacts I-J and I-(J+1) occur simultaneously.
5672 C The system loses extra energy.
5673 c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
5678 c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5679 c & ' jj=',jj,' kk=',kk
5681 C Contacts I-J and (I+1)-J occur simultaneously.
5682 C The system loses extra energy.
5683 c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
5690 c------------------------------------------------------------------------------
5691 subroutine multibody_eello(ecorr,ecorr5,ecorr6,eturn6,n_corr,
5693 C This subroutine calculates multi-body contributions to hydrogen-bonding
5694 implicit real*8 (a-h,o-z)
5695 include 'DIMENSIONS'
5696 include 'DIMENSIONS.ZSCOPT'
5697 include 'COMMON.IOUNITS'
5699 include 'COMMON.INFO'
5701 include 'COMMON.FFIELD'
5702 include 'COMMON.DERIV'
5703 include 'COMMON.INTERACT'
5704 include 'COMMON.CONTACTS'
5706 parameter (max_cont=maxconts)
5707 parameter (max_dim=2*(8*3+2))
5708 parameter (msglen1=max_cont*max_dim*4)
5709 parameter (msglen2=2*msglen1)
5710 integer source,CorrelType,CorrelID,Error
5711 double precision buffer(max_cont,max_dim)
5713 double precision gx(3),gx1(3)
5716 C Set lprn=.true. for debugging
5722 if (fgProcs.le.1) goto 30
5724 write (iout,'(a)') 'Contact function values:'
5726 write (iout,'(2i3,50(1x,i2,f5.2))')
5727 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5728 & j=1,num_cont_hb(i))
5731 C Caution! Following code assumes that electrostatic interactions concerning
5732 C a given atom are split among at most two processors!
5742 cd write (iout,*) 'MyRank',MyRank,' mm',mm
5745 cd write (iout,*) 'Sending: MyRank',MyRank,' mm',mm,' ldone',ldone
5746 if (MyRank.gt.0) then
5747 C Send correlation contributions to the preceding processor
5749 nn=num_cont_hb(iatel_s)
5750 call pack_buffer(max_cont,max_dim,iatel_s,0,buffer)
5751 cd write (iout,*) 'The BUFFER array:'
5753 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,26)
5755 if (ielstart(iatel_s).gt.iatel_s+ispp) then
5757 call pack_buffer(max_cont,max_dim,iatel_s+1,26,buffer)
5758 C Clear the contacts of the atom passed to the neighboring processor
5759 nn=num_cont_hb(iatel_s+1)
5761 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j+26),j=1,26)
5763 num_cont_hb(iatel_s)=0
5765 cd write (iout,*) 'Processor ',MyID,MyRank,
5766 cd & ' is sending correlation contribution to processor',MyID-1,
5767 cd & ' msglen=',msglen
5768 cd write (*,*) 'Processor ',MyID,MyRank,
5769 cd & ' is sending correlation contribution to processor',MyID-1,
5770 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5771 call mp_bsend(buffer,msglen,MyID-1,CorrelType,CorrelID)
5772 cd write (iout,*) 'Processor ',MyID,
5773 cd & ' has sent correlation contribution to processor',MyID-1,
5774 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5775 cd write (*,*) 'Processor ',MyID,
5776 cd & ' has sent correlation contribution to processor',MyID-1,
5777 cd & ' msglen=',msglen,' CorrelID=',CorrelID
5779 endif ! (MyRank.gt.0)
5783 cd write (iout,*) 'Receiving: MyRank',MyRank,' mm',mm,' ldone',ldone
5784 if (MyRank.lt.fgProcs-1) then
5785 C Receive correlation contributions from the next processor
5787 if (ielend(iatel_e).lt.nct-1) msglen=msglen2
5788 cd write (iout,*) 'Processor',MyID,
5789 cd & ' is receiving correlation contribution from processor',MyID+1,
5790 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5791 cd write (*,*) 'Processor',MyID,
5792 cd & ' is receiving correlation contribution from processor',MyID+1,
5793 cd & ' msglen=',msglen,' CorrelType=',CorrelType
5795 do while (nbytes.le.0)
5796 call mp_probe(MyID+1,CorrelType,nbytes)
5798 cd print *,'Processor',MyID,' msglen',msglen,' nbytes',nbytes
5799 call mp_brecv(buffer,msglen,MyID+1,CorrelType,nbytes)
5800 cd write (iout,*) 'Processor',MyID,
5801 cd & ' has received correlation contribution from processor',MyID+1,
5802 cd & ' msglen=',msglen,' nbytes=',nbytes
5803 cd write (iout,*) 'The received BUFFER array:'
5805 cd write (iout,'(i2,9(3f8.3,2x))') i,(buffer(i,j),j=1,52)
5807 if (msglen.eq.msglen1) then
5808 call unpack_buffer(max_cont,max_dim,iatel_e+1,0,buffer)
5809 else if (msglen.eq.msglen2) then
5810 call unpack_buffer(max_cont,max_dim,iatel_e,0,buffer)
5811 call unpack_buffer(max_cont,max_dim,iatel_e+1,26,buffer)
5814 & 'ERROR!!!! message length changed while processing correlations.'
5816 & 'ERROR!!!! message length changed while processing correlations.'
5817 call mp_stopall(Error)
5818 endif ! msglen.eq.msglen1
5819 endif ! MyRank.lt.fgProcs-1
5826 write (iout,'(a)') 'Contact function values:'
5828 write (iout,'(2i3,50(1x,i2,f5.2))')
5829 & i,num_cont_hb(i),(jcont_hb(j,i),facont_hb(j,i),
5830 & j=1,num_cont_hb(i))
5836 C Remove the loop below after debugging !!!
5843 C Calculate the dipole-dipole interaction energies
5844 if (wcorr6.gt.0.0d0 .or. wturn6.gt.0.0d0) then
5845 do i=iatel_s,iatel_e+1
5846 num_conti=num_cont_hb(i)
5853 C Calculate the local-electrostatic correlation terms
5854 do i=iatel_s,iatel_e+1
5856 num_conti=num_cont_hb(i)
5857 num_conti1=num_cont_hb(i+1)
5862 c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5863 c & ' jj=',jj,' kk=',kk
5864 if (j1.eq.j+1 .or. j1.eq.j-1) then
5865 C Contacts I-J and (I+1)-(J+1) or (I+1)-(J-1) occur simultaneously.
5866 C The system gains extra energy.
5868 sqd1=dsqrt(d_cont(jj,i))
5869 sqd2=dsqrt(d_cont(kk,i1))
5870 sred_geom = sqd1*sqd2
5871 IF (sred_geom.lt.cutoff_corr) THEN
5872 call gcont(sred_geom,r0_corr,1.0D0,delt_corr,
5874 c write (*,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5875 c & ' jj=',jj,' kk=',kk
5876 fac_prim1=0.5d0*sqd2/sqd1*fprimcont
5877 fac_prim2=0.5d0*sqd1/sqd2*fprimcont
5879 g_contij(l,1)=fac_prim1*grij_hb_cont(l,jj,i)
5880 g_contij(l,2)=fac_prim2*grij_hb_cont(l,kk,i1)
5883 cd write (iout,*) 'sred_geom=',sred_geom,
5884 cd & ' ekont=',ekont,' fprim=',fprimcont
5885 call calc_eello(i,j,i+1,j1,jj,kk)
5886 if (wcorr4.gt.0.0d0)
5887 & ecorr=ecorr+eello4(i,j,i+1,j1,jj,kk)
5888 if (wcorr5.gt.0.0d0)
5889 & ecorr5=ecorr5+eello5(i,j,i+1,j1,jj,kk)
5890 c print *,"wcorr5",ecorr5
5891 cd write(2,*)'wcorr6',wcorr6,' wturn6',wturn6
5892 cd write(2,*)'ijkl',i,j,i+1,j1
5893 if (wcorr6.gt.0.0d0 .and. (j.ne.i+4 .or. j1.ne.i+3
5894 & .or. wturn6.eq.0.0d0))then
5895 cd write (iout,*) '******ecorr6: i,j,i+1,j1',i,j,i+1,j1
5896 ecorr6=ecorr6+eello6(i,j,i+1,j1,jj,kk)
5897 cd write (iout,*) 'ecorr',ecorr,' ecorr5=',ecorr5,
5898 cd & 'ecorr6=',ecorr6
5899 cd write (iout,'(4e15.5)') sred_geom,
5900 cd & dabs(eello4(i,j,i+1,j1,jj,kk)),
5901 cd & dabs(eello5(i,j,i+1,j1,jj,kk)),
5902 cd & dabs(eello6(i,j,i+1,j1,jj,kk))
5903 else if (wturn6.gt.0.0d0
5904 & .and. (j.eq.i+4 .and. j1.eq.i+3)) then
5905 cd write (iout,*) '******eturn6: i,j,i+1,j1',i,j,i+1,j1
5906 eturn6=eturn6+eello_turn6(i,jj,kk)
5907 cd write (2,*) 'multibody_eello:eturn6',eturn6
5911 else if (j1.eq.j) then
5912 C Contacts I-J and I-(J+1) occur simultaneously.
5913 C The system loses extra energy.
5914 c ecorr=ecorr+ehbcorr(i,j,i+1,j,jj,kk,0.60D0,-0.40D0)
5919 c write (iout,*) 'i=',i,' j=',j,' i1=',i1,' j1=',j1,
5920 c & ' jj=',jj,' kk=',kk
5922 C Contacts I-J and (I+1)-J occur simultaneously.
5923 C The system loses extra energy.
5924 c ecorr=ecorr+ehbcorr(i,j,i,j+1,jj,kk,0.60D0,-0.40D0)
5931 c------------------------------------------------------------------------------
5932 double precision function ehbcorr(i,j,k,l,jj,kk,coeffp,coeffm)
5933 implicit real*8 (a-h,o-z)
5934 include 'DIMENSIONS'
5935 include 'COMMON.IOUNITS'
5936 include 'COMMON.DERIV'
5937 include 'COMMON.INTERACT'
5938 include 'COMMON.CONTACTS'
5939 double precision gx(3),gx1(3)
5949 ees=-(coeffp*ees0pij*ees0pkl+coeffm*ees0mij*ees0mkl)
5950 cd ees=-(coeffp*ees0pkl+coeffm*ees0mkl)
5951 C Following 4 lines for diagnostics.
5956 cd write (iout,*)'Contacts have occurred for peptide groups',i,j,
5958 cd write (iout,*)'Contacts have occurred for peptide groups',
5959 cd & i,j,' fcont:',eij,' eij',' eesij',ees0pij,ees0mij,' and ',k,l
5960 cd & ,' fcont ',ekl,' eeskl',ees0pkl,ees0mkl,' ees=',ees
5961 C Calculate the multi-body contribution to energy.
5962 ecorr=ecorr+ekont*ees
5964 C Calculate multi-body contributions to the gradient.
5966 ghalf=0.5D0*ees*ekl*gacont_hbr(ll,jj,i)
5967 gradcorr(ll,i)=gradcorr(ll,i)+ghalf
5968 & -ekont*(coeffp*ees0pkl*gacontp_hb1(ll,jj,i)+
5969 & coeffm*ees0mkl*gacontm_hb1(ll,jj,i))
5970 gradcorr(ll,j)=gradcorr(ll,j)+ghalf
5971 & -ekont*(coeffp*ees0pkl*gacontp_hb2(ll,jj,i)+
5972 & coeffm*ees0mkl*gacontm_hb2(ll,jj,i))
5973 ghalf=0.5D0*ees*eij*gacont_hbr(ll,kk,k)
5974 gradcorr(ll,k)=gradcorr(ll,k)+ghalf
5975 & -ekont*(coeffp*ees0pij*gacontp_hb1(ll,kk,k)+
5976 & coeffm*ees0mij*gacontm_hb1(ll,kk,k))
5977 gradcorr(ll,l)=gradcorr(ll,l)+ghalf
5978 & -ekont*(coeffp*ees0pij*gacontp_hb2(ll,kk,k)+
5979 & coeffm*ees0mij*gacontm_hb2(ll,kk,k))
5983 gradcorr(ll,m)=gradcorr(ll,m)+
5984 & ees*ekl*gacont_hbr(ll,jj,i)-
5985 & ekont*(coeffp*ees0pkl*gacontp_hb3(ll,jj,i)+
5986 & coeffm*ees0mkl*gacontm_hb3(ll,jj,i))
5991 gradcorr(ll,m)=gradcorr(ll,m)+
5992 & ees*eij*gacont_hbr(ll,kk,k)-
5993 & ekont*(coeffp*ees0pij*gacontp_hb3(ll,kk,k)+
5994 & coeffm*ees0mij*gacontm_hb3(ll,kk,k))
6001 C---------------------------------------------------------------------------
6002 subroutine dipole(i,j,jj)
6003 implicit real*8 (a-h,o-z)
6004 include 'DIMENSIONS'
6005 include 'DIMENSIONS.ZSCOPT'
6006 include 'COMMON.IOUNITS'
6007 include 'COMMON.CHAIN'
6008 include 'COMMON.FFIELD'
6009 include 'COMMON.DERIV'
6010 include 'COMMON.INTERACT'
6011 include 'COMMON.CONTACTS'
6012 include 'COMMON.TORSION'
6013 include 'COMMON.VAR'
6014 include 'COMMON.GEO'
6015 dimension dipi(2,2),dipj(2,2),dipderi(2),dipderj(2),auxvec(2),
6017 iti1 = itortyp(itype(i+1))
6018 if (j.lt.nres-1) then
6019 itj1 = itortyp(itype(j+1))
6024 dipi(iii,1)=Ub2(iii,i)
6025 dipderi(iii)=Ub2der(iii,i)
6026 dipi(iii,2)=b1(iii,iti1)
6027 dipj(iii,1)=Ub2(iii,j)
6028 dipderj(iii)=Ub2der(iii,j)
6029 dipj(iii,2)=b1(iii,itj1)
6033 call matvec2(a_chuj(1,1,jj,i),dipj(1,iii),auxvec(1))
6036 dip(kkk,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
6039 if (.not.calc_grad) return
6044 call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),dipj(1,iii),
6048 dipderx(lll,kkk,mmm,jj,i)=scalar2(dipi(1,jjj),auxvec(1))
6053 call transpose2(a_chuj(1,1,jj,i),auxmat(1,1))
6054 call matvec2(auxmat(1,1),dipderi(1),auxvec(1))
6056 dipderg(iii,jj,i)=scalar2(auxvec(1),dipj(1,iii))
6058 call matvec2(a_chuj(1,1,jj,i),dipderj(1),auxvec(1))
6060 dipderg(iii+2,jj,i)=scalar2(auxvec(1),dipi(1,iii))
6064 C---------------------------------------------------------------------------
6065 subroutine calc_eello(i,j,k,l,jj,kk)
6067 C This subroutine computes matrices and vectors needed to calculate
6068 C the fourth-, fifth-, and sixth-order local-electrostatic terms.
6070 implicit real*8 (a-h,o-z)
6071 include 'DIMENSIONS'
6072 include 'DIMENSIONS.ZSCOPT'
6073 include 'COMMON.IOUNITS'
6074 include 'COMMON.CHAIN'
6075 include 'COMMON.DERIV'
6076 include 'COMMON.INTERACT'
6077 include 'COMMON.CONTACTS'
6078 include 'COMMON.TORSION'
6079 include 'COMMON.VAR'
6080 include 'COMMON.GEO'
6081 include 'COMMON.FFIELD'
6082 double precision aa1(2,2),aa2(2,2),aa1t(2,2),aa2t(2,2),
6083 & aa1tder(2,2,3,5),aa2tder(2,2,3,5),auxmat(2,2)
6086 cd write (iout,*) 'calc_eello: i=',i,' j=',j,' k=',k,' l=',l,
6087 cd & ' jj=',jj,' kk=',kk
6088 cd if (i.ne.2 .or. j.ne.4 .or. k.ne.3 .or. l.ne.5) return
6091 aa1(iii,jjj)=a_chuj(iii,jjj,jj,i)
6092 aa2(iii,jjj)=a_chuj(iii,jjj,kk,k)
6095 call transpose2(aa1(1,1),aa1t(1,1))
6096 call transpose2(aa2(1,1),aa2t(1,1))
6099 call transpose2(a_chuj_der(1,1,lll,kkk,jj,i),
6100 & aa1tder(1,1,lll,kkk))
6101 call transpose2(a_chuj_der(1,1,lll,kkk,kk,k),
6102 & aa2tder(1,1,lll,kkk))
6106 C parallel orientation of the two CA-CA-CA frames.
6108 iti=itortyp(itype(i))
6112 itk1=itortyp(itype(k+1))
6113 itj=itortyp(itype(j))
6114 if (l.lt.nres-1) then
6115 itl1=itortyp(itype(l+1))
6119 C A1 kernel(j+1) A2T
6121 cd write (iout,'(3f10.5,5x,3f10.5)')
6122 cd & (EUg(iii,jjj,k),jjj=1,2),(EUg(iii,jjj,l),jjj=1,2)
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.,EUg(1,1,l),EUgder(1,1,l),
6126 & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
6127 C Following matrices are needed only for 6-th order cumulants
6128 IF (wcorr6.gt.0.0d0) THEN
6129 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6130 & aa2tder(1,1,1,1),1,.false.,EUgC(1,1,l),EUgCder(1,1,l),
6131 & AECA(1,1,1),AECAderg(1,1,1),AECAderx(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.,Ug2DtEUg(1,1,l),
6134 & Ug2DtEUgder(1,1,1,l),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
6135 & ADtEAderx(1,1,1,1,1,1))
6137 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6138 & aa2tder(1,1,1,1),2,.false.,DtUg2EUg(1,1,l),
6139 & DtUg2EUgder(1,1,1,l),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
6140 & ADtEA1derx(1,1,1,1,1,1))
6142 C End 6-th order cumulants
6145 cd write (2,*) 'In calc_eello6'
6147 cd write (2,*) 'iii=',iii
6149 cd write (2,*) 'kkk=',kkk
6151 cd write (2,'(3(2f10.5),5x)')
6152 cd & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
6157 call transpose2(EUgder(1,1,k),auxmat(1,1))
6158 call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
6159 call transpose2(EUg(1,1,k),auxmat(1,1))
6160 call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
6161 call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
6165 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
6166 & EAEAderx(1,1,lll,kkk,iii,1))
6170 C A1T kernel(i+1) A2
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.,EUg(1,1,k),EUgder(1,1,k),
6173 & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
6174 C Following matrices are needed only for 6-th order cumulants
6175 IF (wcorr6.gt.0.0d0) THEN
6176 call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
6177 & a_chuj_der(1,1,1,1,kk,k),1,.false.,EUgC(1,1,k),EUgCder(1,1,k),
6178 & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
6179 call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
6180 & a_chuj_der(1,1,1,1,kk,k),2,.false.,Ug2DtEUg(1,1,k),
6181 & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
6182 & ADtEAderx(1,1,1,1,1,2))
6183 call kernel(aa1t(1,1),aa2(1,1),aa1tder(1,1,1,1),
6184 & a_chuj_der(1,1,1,1,kk,k),2,.false.,DtUg2EUg(1,1,k),
6185 & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
6186 & ADtEA1derx(1,1,1,1,1,2))
6188 C End 6-th order cumulants
6189 call transpose2(EUgder(1,1,l),auxmat(1,1))
6190 call matmat2(auxmat(1,1),AEA(1,1,2),EAEAderg(1,1,1,2))
6191 call transpose2(EUg(1,1,l),auxmat(1,1))
6192 call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
6193 call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
6197 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6198 & EAEAderx(1,1,lll,kkk,iii,2))
6203 C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
6204 C They are needed only when the fifth- or the sixth-order cumulants are
6206 IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0) THEN
6207 call transpose2(AEA(1,1,1),auxmat(1,1))
6208 call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
6209 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
6210 call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
6211 call transpose2(AEAderg(1,1,1),auxmat(1,1))
6212 call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
6213 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
6214 call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
6215 call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
6216 call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
6217 call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
6218 call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
6219 call transpose2(AEA(1,1,2),auxmat(1,1))
6220 call matvec2(auxmat(1,1),b1(1,itj),AEAb1(1,1,2))
6221 call matvec2(auxmat(1,1),Ub2(1,j),AEAb2(1,1,2))
6222 call matvec2(auxmat(1,1),Ub2der(1,j),AEAb2derg(1,2,1,2))
6223 call transpose2(AEAderg(1,1,2),auxmat(1,1))
6224 call matvec2(auxmat(1,1),b1(1,itj),AEAb1derg(1,1,2))
6225 call matvec2(auxmat(1,1),Ub2(1,j),AEAb2derg(1,1,1,2))
6226 call matvec2(AEA(1,1,2),b1(1,itl1),AEAb1(1,2,2))
6227 call matvec2(AEAderg(1,1,2),b1(1,itl1),AEAb1derg(1,2,2))
6228 call matvec2(AEA(1,1,2),Ub2(1,l+1),AEAb2(1,2,2))
6229 call matvec2(AEAderg(1,1,2),Ub2(1,l+1),AEAb2derg(1,1,2,2))
6230 call matvec2(AEA(1,1,2),Ub2der(1,l+1),AEAb2derg(1,2,2,2))
6231 C Calculate the Cartesian derivatives of the vectors.
6235 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
6236 call matvec2(auxmat(1,1),b1(1,iti),
6237 & AEAb1derx(1,lll,kkk,iii,1,1))
6238 call matvec2(auxmat(1,1),Ub2(1,i),
6239 & AEAb2derx(1,lll,kkk,iii,1,1))
6240 call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
6241 & AEAb1derx(1,lll,kkk,iii,2,1))
6242 call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
6243 & AEAb2derx(1,lll,kkk,iii,2,1))
6244 call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
6245 call matvec2(auxmat(1,1),b1(1,itj),
6246 & AEAb1derx(1,lll,kkk,iii,1,2))
6247 call matvec2(auxmat(1,1),Ub2(1,j),
6248 & AEAb2derx(1,lll,kkk,iii,1,2))
6249 call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
6250 & AEAb1derx(1,lll,kkk,iii,2,2))
6251 call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,l+1),
6252 & AEAb2derx(1,lll,kkk,iii,2,2))
6259 C Antiparallel orientation of the two CA-CA-CA frames.
6261 iti=itortyp(itype(i))
6265 itk1=itortyp(itype(k+1))
6266 itl=itortyp(itype(l))
6267 itj=itortyp(itype(j))
6268 if (j.lt.nres-1) then
6269 itj1=itortyp(itype(j+1))
6273 C A2 kernel(j-1)T A1T
6274 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6275 & aa2tder(1,1,1,1),1,.true.,EUg(1,1,j),EUgder(1,1,j),
6276 & AEA(1,1,1),AEAderg(1,1,1),AEAderx(1,1,1,1,1,1))
6277 C Following matrices are needed only for 6-th order cumulants
6278 IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
6279 & j.eq.i+4 .and. l.eq.i+3)) THEN
6280 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6281 & aa2tder(1,1,1,1),1,.true.,EUgC(1,1,j),EUgCder(1,1,j),
6282 & AECA(1,1,1),AECAderg(1,1,1),AECAderx(1,1,1,1,1,1))
6283 call kernel(aa2(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6284 & aa2tder(1,1,1,1),2,.true.,Ug2DtEUg(1,1,j),
6285 & Ug2DtEUgder(1,1,1,j),ADtEA(1,1,1),ADtEAderg(1,1,1,1),
6286 & ADtEAderx(1,1,1,1,1,1))
6287 call kernel(aa1(1,1),aa2t(1,1),a_chuj_der(1,1,1,1,jj,i),
6288 & aa2tder(1,1,1,1),2,.true.,DtUg2EUg(1,1,j),
6289 & DtUg2EUgder(1,1,1,j),ADtEA1(1,1,1),ADtEA1derg(1,1,1,1),
6290 & ADtEA1derx(1,1,1,1,1,1))
6292 C End 6-th order cumulants
6293 call transpose2(EUgder(1,1,k),auxmat(1,1))
6294 call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,1,1))
6295 call transpose2(EUg(1,1,k),auxmat(1,1))
6296 call matmat2(auxmat(1,1),AEA(1,1,1),EAEA(1,1,1))
6297 call matmat2(auxmat(1,1),AEAderg(1,1,1),EAEAderg(1,1,2,1))
6301 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
6302 & EAEAderx(1,1,lll,kkk,iii,1))
6306 C A2T kernel(i+1)T A1
6307 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6308 & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUg(1,1,k),EUgder(1,1,k),
6309 & AEA(1,1,2),AEAderg(1,1,2),AEAderx(1,1,1,1,1,2))
6310 C Following matrices are needed only for 6-th order cumulants
6311 IF (wcorr6.gt.0.0d0 .or. (wturn6.gt.0.0d0 .and.
6312 & j.eq.i+4 .and. l.eq.i+3)) THEN
6313 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6314 & a_chuj_der(1,1,1,1,jj,i),1,.true.,EUgC(1,1,k),EUgCder(1,1,k),
6315 & AECA(1,1,2),AECAderg(1,1,2),AECAderx(1,1,1,1,1,2))
6316 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6317 & a_chuj_der(1,1,1,1,jj,i),2,.true.,Ug2DtEUg(1,1,k),
6318 & Ug2DtEUgder(1,1,1,k),ADtEA(1,1,2),ADtEAderg(1,1,1,2),
6319 & ADtEAderx(1,1,1,1,1,2))
6320 call kernel(aa2t(1,1),aa1(1,1),aa2tder(1,1,1,1),
6321 & a_chuj_der(1,1,1,1,jj,i),2,.true.,DtUg2EUg(1,1,k),
6322 & DtUg2EUgder(1,1,1,k),ADtEA1(1,1,2),ADtEA1derg(1,1,1,2),
6323 & ADtEA1derx(1,1,1,1,1,2))
6325 C End 6-th order cumulants
6326 call transpose2(EUgder(1,1,j),auxmat(1,1))
6327 call matmat2(auxmat(1,1),AEA(1,1,1),EAEAderg(1,1,2,2))
6328 call transpose2(EUg(1,1,j),auxmat(1,1))
6329 call matmat2(auxmat(1,1),AEA(1,1,2),EAEA(1,1,2))
6330 call matmat2(auxmat(1,1),AEAderg(1,1,2),EAEAderg(1,1,2,2))
6334 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6335 & EAEAderx(1,1,lll,kkk,iii,2))
6340 C Calculate the vectors and their derivatives in virtual-bond dihedral angles.
6341 C They are needed only when the fifth- or the sixth-order cumulants are
6343 IF (wcorr5.gt.0.0d0 .or. wcorr6.gt.0.0d0 .or.
6344 & (wturn6.gt.0.0d0 .and. j.eq.i+4 .and. l.eq.i+3)) THEN
6345 call transpose2(AEA(1,1,1),auxmat(1,1))
6346 call matvec2(auxmat(1,1),b1(1,iti),AEAb1(1,1,1))
6347 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2(1,1,1))
6348 call matvec2(auxmat(1,1),Ub2der(1,i),AEAb2derg(1,2,1,1))
6349 call transpose2(AEAderg(1,1,1),auxmat(1,1))
6350 call matvec2(auxmat(1,1),b1(1,iti),AEAb1derg(1,1,1))
6351 call matvec2(auxmat(1,1),Ub2(1,i),AEAb2derg(1,1,1,1))
6352 call matvec2(AEA(1,1,1),b1(1,itk1),AEAb1(1,2,1))
6353 call matvec2(AEAderg(1,1,1),b1(1,itk1),AEAb1derg(1,2,1))
6354 call matvec2(AEA(1,1,1),Ub2(1,k+1),AEAb2(1,2,1))
6355 call matvec2(AEAderg(1,1,1),Ub2(1,k+1),AEAb2derg(1,1,2,1))
6356 call matvec2(AEA(1,1,1),Ub2der(1,k+1),AEAb2derg(1,2,2,1))
6357 call transpose2(AEA(1,1,2),auxmat(1,1))
6358 call matvec2(auxmat(1,1),b1(1,itj1),AEAb1(1,1,2))
6359 call matvec2(auxmat(1,1),Ub2(1,l),AEAb2(1,1,2))
6360 call matvec2(auxmat(1,1),Ub2der(1,l),AEAb2derg(1,2,1,2))
6361 call transpose2(AEAderg(1,1,2),auxmat(1,1))
6362 call matvec2(auxmat(1,1),b1(1,itl),AEAb1(1,1,2))
6363 call matvec2(auxmat(1,1),Ub2(1,l),AEAb2derg(1,1,1,2))
6364 call matvec2(AEA(1,1,2),b1(1,itj1),AEAb1(1,2,2))
6365 call matvec2(AEAderg(1,1,2),b1(1,itj1),AEAb1derg(1,2,2))
6366 call matvec2(AEA(1,1,2),Ub2(1,j),AEAb2(1,2,2))
6367 call matvec2(AEAderg(1,1,2),Ub2(1,j),AEAb2derg(1,1,2,2))
6368 call matvec2(AEA(1,1,2),Ub2der(1,j),AEAb2derg(1,2,2,2))
6369 C Calculate the Cartesian derivatives of the vectors.
6373 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1))
6374 call matvec2(auxmat(1,1),b1(1,iti),
6375 & AEAb1derx(1,lll,kkk,iii,1,1))
6376 call matvec2(auxmat(1,1),Ub2(1,i),
6377 & AEAb2derx(1,lll,kkk,iii,1,1))
6378 call matvec2(AEAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
6379 & AEAb1derx(1,lll,kkk,iii,2,1))
6380 call matvec2(AEAderx(1,1,lll,kkk,iii,1),Ub2(1,k+1),
6381 & AEAb2derx(1,lll,kkk,iii,2,1))
6382 call transpose2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1))
6383 call matvec2(auxmat(1,1),b1(1,itl),
6384 & AEAb1derx(1,lll,kkk,iii,1,2))
6385 call matvec2(auxmat(1,1),Ub2(1,l),
6386 & AEAb2derx(1,lll,kkk,iii,1,2))
6387 call matvec2(AEAderx(1,1,lll,kkk,iii,2),b1(1,itj1),
6388 & AEAb1derx(1,lll,kkk,iii,2,2))
6389 call matvec2(AEAderx(1,1,lll,kkk,iii,2),Ub2(1,j),
6390 & AEAb2derx(1,lll,kkk,iii,2,2))
6399 C---------------------------------------------------------------------------
6400 subroutine kernel(aa1,aa2t,aa1derx,aa2tderx,nderg,transp,
6401 & KK,KKderg,AKA,AKAderg,AKAderx)
6405 double precision aa1(2,2),aa2t(2,2),aa1derx(2,2,3,5),
6406 & aa2tderx(2,2,3,5),KK(2,2),KKderg(2,2,nderg),AKA(2,2),
6407 & AKAderg(2,2,nderg),AKAderx(2,2,3,5,2)
6412 call prodmat3(aa1(1,1),aa2t(1,1),KK(1,1),transp,AKA(1,1))
6414 call prodmat3(aa1(1,1),aa2t(1,1),KKderg(1,1,iii),transp,
6417 cd if (lprn) write (2,*) 'In kernel'
6419 cd if (lprn) write (2,*) 'kkk=',kkk
6421 call prodmat3(aa1derx(1,1,lll,kkk),aa2t(1,1),
6422 & KK(1,1),transp,AKAderx(1,1,lll,kkk,1))
6424 cd write (2,*) 'lll=',lll
6425 cd write (2,*) 'iii=1'
6427 cd write (2,'(3(2f10.5),5x)')
6428 cd & (AKAderx(jjj,mmm,lll,kkk,1),mmm=1,2)
6431 call prodmat3(aa1(1,1),aa2tderx(1,1,lll,kkk),
6432 & KK(1,1),transp,AKAderx(1,1,lll,kkk,2))
6434 cd write (2,*) 'lll=',lll
6435 cd write (2,*) 'iii=2'
6437 cd write (2,'(3(2f10.5),5x)')
6438 cd & (AKAderx(jjj,mmm,lll,kkk,2),mmm=1,2)
6445 C---------------------------------------------------------------------------
6446 double precision function eello4(i,j,k,l,jj,kk)
6447 implicit real*8 (a-h,o-z)
6448 include 'DIMENSIONS'
6449 include 'DIMENSIONS.ZSCOPT'
6450 include 'COMMON.IOUNITS'
6451 include 'COMMON.CHAIN'
6452 include 'COMMON.DERIV'
6453 include 'COMMON.INTERACT'
6454 include 'COMMON.CONTACTS'
6455 include 'COMMON.TORSION'
6456 include 'COMMON.VAR'
6457 include 'COMMON.GEO'
6458 double precision pizda(2,2),ggg1(3),ggg2(3)
6459 cd if (i.ne.1 .or. j.ne.5 .or. k.ne.2 .or.l.ne.4) then
6463 cd print *,'eello4:',i,j,k,l,jj,kk
6464 cd write (2,*) 'i',i,' j',j,' k',k,' l',l
6465 cd call checkint4(i,j,k,l,jj,kk,eel4_num)
6466 cold eij=facont_hb(jj,i)
6467 cold ekl=facont_hb(kk,k)
6469 eel4=-EAEA(1,1,1)-EAEA(2,2,1)
6471 cd eel41=-EAEA(1,1,2)-EAEA(2,2,2)
6472 gcorr_loc(k-1)=gcorr_loc(k-1)
6473 & -ekont*(EAEAderg(1,1,1,1)+EAEAderg(2,2,1,1))
6475 gcorr_loc(l-1)=gcorr_loc(l-1)
6476 & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
6478 gcorr_loc(j-1)=gcorr_loc(j-1)
6479 & -ekont*(EAEAderg(1,1,2,1)+EAEAderg(2,2,2,1))
6484 derx(lll,kkk,iii)=-EAEAderx(1,1,lll,kkk,iii,1)
6485 & -EAEAderx(2,2,lll,kkk,iii,1)
6486 cd derx(lll,kkk,iii)=0.0d0
6490 cd gcorr_loc(l-1)=0.0d0
6491 cd gcorr_loc(j-1)=0.0d0
6492 cd gcorr_loc(k-1)=0.0d0
6494 cd write (iout,*)'Contacts have occurred for peptide groups',
6495 cd & i,j,' fcont:',eij,' eij',' and ',k,l,
6496 cd & ' fcont ',ekl,' eel4=',eel4,' eel4_num',16*eel4_num
6497 if (j.lt.nres-1) then
6504 if (l.lt.nres-1) then
6512 cold ghalf=0.5d0*eel4*ekl*gacont_hbr(ll,jj,i)
6513 ggg1(ll)=eel4*g_contij(ll,1)
6514 ggg2(ll)=eel4*g_contij(ll,2)
6515 ghalf=0.5d0*ggg1(ll)
6517 gradcorr(ll,i)=gradcorr(ll,i)+ghalf+ekont*derx(ll,2,1)
6518 gradcorr(ll,i+1)=gradcorr(ll,i+1)+ekont*derx(ll,3,1)
6519 gradcorr(ll,j)=gradcorr(ll,j)+ghalf+ekont*derx(ll,4,1)
6520 gradcorr(ll,j1)=gradcorr(ll,j1)+ekont*derx(ll,5,1)
6521 cold ghalf=0.5d0*eel4*eij*gacont_hbr(ll,kk,k)
6522 ghalf=0.5d0*ggg2(ll)
6524 gradcorr(ll,k)=gradcorr(ll,k)+ghalf+ekont*derx(ll,2,2)
6525 gradcorr(ll,k+1)=gradcorr(ll,k+1)+ekont*derx(ll,3,2)
6526 gradcorr(ll,l)=gradcorr(ll,l)+ghalf+ekont*derx(ll,4,2)
6527 gradcorr(ll,l1)=gradcorr(ll,l1)+ekont*derx(ll,5,2)
6532 cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*ekl*gacont_hbr(ll,jj,i)
6533 gradcorr(ll,m)=gradcorr(ll,m)+ggg1(ll)
6538 cold gradcorr(ll,m)=gradcorr(ll,m)+eel4*eij*gacont_hbr(ll,kk,k)
6539 gradcorr(ll,m)=gradcorr(ll,m)+ggg2(ll)
6545 gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,1)
6550 gradcorr(ll,m)=gradcorr(ll,m)+ekont*derx(ll,1,2)
6554 cd write (2,*) iii,gcorr_loc(iii)
6558 cd write (2,*) 'ekont',ekont
6559 cd write (iout,*) 'eello4',ekont*eel4
6562 C---------------------------------------------------------------------------
6563 double precision function eello5(i,j,k,l,jj,kk)
6564 implicit real*8 (a-h,o-z)
6565 include 'DIMENSIONS'
6566 include 'DIMENSIONS.ZSCOPT'
6567 include 'COMMON.IOUNITS'
6568 include 'COMMON.CHAIN'
6569 include 'COMMON.DERIV'
6570 include 'COMMON.INTERACT'
6571 include 'COMMON.CONTACTS'
6572 include 'COMMON.TORSION'
6573 include 'COMMON.VAR'
6574 include 'COMMON.GEO'
6575 double precision pizda(2,2),auxmat(2,2),auxmat1(2,2),vv(2)
6576 double precision ggg1(3),ggg2(3)
6577 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6582 C /l\ / \ \ / \ / \ / C
6583 C / \ / \ \ / \ / \ / C
6584 C j| o |l1 | o | o| o | | o |o C
6585 C \ |/k\| |/ \| / |/ \| |/ \| C
6586 C \i/ \ / \ / / \ / \ C
6588 C (I) (II) (III) (IV) C
6590 C eello5_1 eello5_2 eello5_3 eello5_4 C
6592 C Antiparallel chains C
6595 C /j\ / \ \ / \ / \ / C
6596 C / \ / \ \ / \ / \ / C
6597 C j1| o |l | o | o| o | | o |o C
6598 C \ |/k\| |/ \| / |/ \| |/ \| C
6599 C \i/ \ / \ / / \ / \ C
6601 C (I) (II) (III) (IV) C
6603 C eello5_1 eello5_2 eello5_3 eello5_4 C
6605 C o denotes a local interaction, vertical lines an electrostatic interaction. C
6607 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6608 cd if (i.ne.2 .or. j.ne.6 .or. k.ne.3 .or. l.ne.5) then
6613 cd & 'EELLO5: Contacts have occurred for peptide groups',i,j,
6615 itk=itortyp(itype(k))
6616 itl=itortyp(itype(l))
6617 itj=itortyp(itype(j))
6622 cd call checkint5(i,j,k,l,jj,kk,eel5_1_num,eel5_2_num,
6623 cd & eel5_3_num,eel5_4_num)
6627 derx(lll,kkk,iii)=0.0d0
6631 cd eij=facont_hb(jj,i)
6632 cd ekl=facont_hb(kk,k)
6634 cd write (iout,*)'Contacts have occurred for peptide groups',
6635 cd & i,j,' fcont:',eij,' eij',' and ',k,l
6637 C Contribution from the graph I.
6638 cd write (2,*) 'AEA ',AEA(1,1,1),AEA(2,1,1),AEA(1,2,1),AEA(2,2,1)
6639 cd write (2,*) 'AEAb2',AEAb2(1,1,1),AEAb2(2,1,1)
6640 call transpose2(EUg(1,1,k),auxmat(1,1))
6641 call matmat2(AEA(1,1,1),auxmat(1,1),pizda(1,1))
6642 vv(1)=pizda(1,1)-pizda(2,2)
6643 vv(2)=pizda(1,2)+pizda(2,1)
6644 eello5_1=scalar2(AEAb2(1,1,1),Ub2(1,k))
6645 & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
6647 C Explicit gradient in virtual-dihedral angles.
6648 if (i.gt.1) g_corr5_loc(i-1)=g_corr5_loc(i-1)
6649 & +ekont*(scalar2(AEAb2derg(1,2,1,1),Ub2(1,k))
6650 & +0.5d0*scalar2(vv(1),Dtobr2der(1,i)))
6651 call transpose2(EUgder(1,1,k),auxmat1(1,1))
6652 call matmat2(AEA(1,1,1),auxmat1(1,1),pizda(1,1))
6653 vv(1)=pizda(1,1)-pizda(2,2)
6654 vv(2)=pizda(1,2)+pizda(2,1)
6655 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6656 & +ekont*(scalar2(AEAb2(1,1,1),Ub2der(1,k))
6657 & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
6658 call matmat2(AEAderg(1,1,1),auxmat(1,1),pizda(1,1))
6659 vv(1)=pizda(1,1)-pizda(2,2)
6660 vv(2)=pizda(1,2)+pizda(2,1)
6662 if (l.lt.nres-1) g_corr5_loc(l-1)=g_corr5_loc(l-1)
6663 & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
6664 & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
6666 if (j.lt.nres-1) g_corr5_loc(j-1)=g_corr5_loc(j-1)
6667 & +ekont*(scalar2(AEAb2derg(1,1,1,1),Ub2(1,k))
6668 & +0.5d0*scalar2(vv(1),Dtobr2(1,i)))
6670 C Cartesian gradient
6674 call matmat2(AEAderx(1,1,lll,kkk,iii,1),auxmat(1,1),
6676 vv(1)=pizda(1,1)-pizda(2,2)
6677 vv(2)=pizda(1,2)+pizda(2,1)
6678 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6679 & +scalar2(AEAb2derx(1,lll,kkk,iii,1,1),Ub2(1,k))
6680 & +0.5d0*scalar2(vv(1),Dtobr2(1,i))
6687 C Contribution from graph II
6688 call transpose2(EE(1,1,itk),auxmat(1,1))
6689 call matmat2(auxmat(1,1),AEA(1,1,1),pizda(1,1))
6690 vv(1)=pizda(1,1)+pizda(2,2)
6691 vv(2)=pizda(2,1)-pizda(1,2)
6692 eello5_2=scalar2(AEAb1(1,2,1),b1(1,itk))
6693 & -0.5d0*scalar2(vv(1),Ctobr(1,k))
6695 C Explicit gradient in virtual-dihedral angles.
6696 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6697 & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,k))
6698 call matmat2(auxmat(1,1),AEAderg(1,1,1),pizda(1,1))
6699 vv(1)=pizda(1,1)+pizda(2,2)
6700 vv(2)=pizda(2,1)-pizda(1,2)
6702 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6703 & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
6704 & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
6706 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6707 & +ekont*(scalar2(AEAb1derg(1,2,1),b1(1,itk))
6708 & -0.5d0*scalar2(vv(1),Ctobr(1,k)))
6710 C Cartesian gradient
6714 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,1),
6716 vv(1)=pizda(1,1)+pizda(2,2)
6717 vv(2)=pizda(2,1)-pizda(1,2)
6718 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6719 & +scalar2(AEAb1derx(1,lll,kkk,iii,2,1),b1(1,itk))
6720 & -0.5d0*scalar2(vv(1),Ctobr(1,k))
6729 C Parallel orientation
6730 C Contribution from graph III
6731 call transpose2(EUg(1,1,l),auxmat(1,1))
6732 call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
6733 vv(1)=pizda(1,1)-pizda(2,2)
6734 vv(2)=pizda(1,2)+pizda(2,1)
6735 eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,l))
6736 & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
6738 C Explicit gradient in virtual-dihedral angles.
6739 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6740 & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,l))
6741 & +0.5d0*scalar2(vv(1),Dtobr2der(1,j)))
6742 call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
6743 vv(1)=pizda(1,1)-pizda(2,2)
6744 vv(2)=pizda(1,2)+pizda(2,1)
6745 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6746 & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,l))
6747 & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
6748 call transpose2(EUgder(1,1,l),auxmat1(1,1))
6749 call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
6750 vv(1)=pizda(1,1)-pizda(2,2)
6751 vv(2)=pizda(1,2)+pizda(2,1)
6752 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6753 & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,l))
6754 & +0.5d0*scalar2(vv(1),Dtobr2(1,j)))
6755 C Cartesian gradient
6759 call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
6761 vv(1)=pizda(1,1)-pizda(2,2)
6762 vv(2)=pizda(1,2)+pizda(2,1)
6763 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6764 & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,l))
6765 & +0.5d0*scalar2(vv(1),Dtobr2(1,j))
6771 C Contribution from graph IV
6773 call transpose2(EE(1,1,itl),auxmat(1,1))
6774 call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
6775 vv(1)=pizda(1,1)+pizda(2,2)
6776 vv(2)=pizda(2,1)-pizda(1,2)
6777 eello5_4=scalar2(AEAb1(1,2,2),b1(1,itl))
6778 & -0.5d0*scalar2(vv(1),Ctobr(1,l))
6780 C Explicit gradient in virtual-dihedral angles.
6781 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6782 & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,l))
6783 call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
6784 vv(1)=pizda(1,1)+pizda(2,2)
6785 vv(2)=pizda(2,1)-pizda(1,2)
6786 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6787 & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itl))
6788 & -0.5d0*scalar2(vv(1),Ctobr(1,l)))
6789 C Cartesian gradient
6793 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6795 vv(1)=pizda(1,1)+pizda(2,2)
6796 vv(2)=pizda(2,1)-pizda(1,2)
6797 derx(lll,kkk,iii)=derx(lll,kkk,iii)
6798 & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itl))
6799 & -0.5d0*scalar2(vv(1),Ctobr(1,l))
6805 C Antiparallel orientation
6806 C Contribution from graph III
6808 call transpose2(EUg(1,1,j),auxmat(1,1))
6809 call matmat2(AEA(1,1,2),auxmat(1,1),pizda(1,1))
6810 vv(1)=pizda(1,1)-pizda(2,2)
6811 vv(2)=pizda(1,2)+pizda(2,1)
6812 eello5_3=scalar2(AEAb2(1,1,2),Ub2(1,j))
6813 & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
6815 C Explicit gradient in virtual-dihedral angles.
6816 g_corr5_loc(l-1)=g_corr5_loc(l-1)
6817 & +ekont*(scalar2(AEAb2derg(1,2,1,2),Ub2(1,j))
6818 & +0.5d0*scalar2(vv(1),Dtobr2der(1,l)))
6819 call matmat2(AEAderg(1,1,2),auxmat(1,1),pizda(1,1))
6820 vv(1)=pizda(1,1)-pizda(2,2)
6821 vv(2)=pizda(1,2)+pizda(2,1)
6822 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6823 & +ekont*(scalar2(AEAb2derg(1,1,1,2),Ub2(1,j))
6824 & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
6825 call transpose2(EUgder(1,1,j),auxmat1(1,1))
6826 call matmat2(AEA(1,1,2),auxmat1(1,1),pizda(1,1))
6827 vv(1)=pizda(1,1)-pizda(2,2)
6828 vv(2)=pizda(1,2)+pizda(2,1)
6829 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6830 & +ekont*(scalar2(AEAb2(1,1,2),Ub2der(1,j))
6831 & +0.5d0*scalar2(vv(1),Dtobr2(1,l)))
6832 C Cartesian gradient
6836 call matmat2(AEAderx(1,1,lll,kkk,iii,2),auxmat(1,1),
6838 vv(1)=pizda(1,1)-pizda(2,2)
6839 vv(2)=pizda(1,2)+pizda(2,1)
6840 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
6841 & +scalar2(AEAb2derx(1,lll,kkk,iii,1,2),Ub2(1,j))
6842 & +0.5d0*scalar2(vv(1),Dtobr2(1,l))
6848 C Contribution from graph IV
6850 call transpose2(EE(1,1,itj),auxmat(1,1))
6851 call matmat2(auxmat(1,1),AEA(1,1,2),pizda(1,1))
6852 vv(1)=pizda(1,1)+pizda(2,2)
6853 vv(2)=pizda(2,1)-pizda(1,2)
6854 eello5_4=scalar2(AEAb1(1,2,2),b1(1,itj))
6855 & -0.5d0*scalar2(vv(1),Ctobr(1,j))
6857 C Explicit gradient in virtual-dihedral angles.
6858 g_corr5_loc(j-1)=g_corr5_loc(j-1)
6859 & -0.5d0*ekont*scalar2(vv(1),Ctobrder(1,j))
6860 call matmat2(auxmat(1,1),AEAderg(1,1,2),pizda(1,1))
6861 vv(1)=pizda(1,1)+pizda(2,2)
6862 vv(2)=pizda(2,1)-pizda(1,2)
6863 g_corr5_loc(k-1)=g_corr5_loc(k-1)
6864 & +ekont*(scalar2(AEAb1derg(1,2,2),b1(1,itj))
6865 & -0.5d0*scalar2(vv(1),Ctobr(1,j)))
6866 C Cartesian gradient
6870 call matmat2(auxmat(1,1),AEAderx(1,1,lll,kkk,iii,2),
6872 vv(1)=pizda(1,1)+pizda(2,2)
6873 vv(2)=pizda(2,1)-pizda(1,2)
6874 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)
6875 & +scalar2(AEAb1derx(1,lll,kkk,iii,2,2),b1(1,itj))
6876 & -0.5d0*scalar2(vv(1),Ctobr(1,j))
6883 eel5=eello5_1+eello5_2+eello5_3+eello5_4
6884 cd if (i.eq.2 .and. j.eq.8 .and. k.eq.3 .and. l.eq.7) then
6885 cd write (2,*) 'ijkl',i,j,k,l
6886 cd write (2,*) 'eello5_1',eello5_1,' eello5_2',eello5_2,
6887 cd & ' eello5_3',eello5_3,' eello5_4',eello5_4
6889 cd write(iout,*) 'eello5_1',eello5_1,' eel5_1_num',16*eel5_1_num
6890 cd write(iout,*) 'eello5_2',eello5_2,' eel5_2_num',16*eel5_2_num
6891 cd write(iout,*) 'eello5_3',eello5_3,' eel5_3_num',16*eel5_3_num
6892 cd write(iout,*) 'eello5_4',eello5_4,' eel5_4_num',16*eel5_4_num
6894 if (j.lt.nres-1) then
6901 if (l.lt.nres-1) then
6911 cd write (2,*) 'eij',eij,' ekl',ekl,' ekont',ekont
6913 ggg1(ll)=eel5*g_contij(ll,1)
6914 ggg2(ll)=eel5*g_contij(ll,2)
6915 cold ghalf=0.5d0*eel5*ekl*gacont_hbr(ll,jj,i)
6916 ghalf=0.5d0*ggg1(ll)
6918 gradcorr5(ll,i)=gradcorr5(ll,i)+ghalf+ekont*derx(ll,2,1)
6919 gradcorr5(ll,i+1)=gradcorr5(ll,i+1)+ekont*derx(ll,3,1)
6920 gradcorr5(ll,j)=gradcorr5(ll,j)+ghalf+ekont*derx(ll,4,1)
6921 gradcorr5(ll,j1)=gradcorr5(ll,j1)+ekont*derx(ll,5,1)
6922 cold ghalf=0.5d0*eel5*eij*gacont_hbr(ll,kk,k)
6923 ghalf=0.5d0*ggg2(ll)
6925 gradcorr5(ll,k)=gradcorr5(ll,k)+ghalf+ekont*derx(ll,2,2)
6926 gradcorr5(ll,k+1)=gradcorr5(ll,k+1)+ekont*derx(ll,3,2)
6927 gradcorr5(ll,l)=gradcorr5(ll,l)+ghalf+ekont*derx(ll,4,2)
6928 gradcorr5(ll,l1)=gradcorr5(ll,l1)+ekont*derx(ll,5,2)
6933 cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*ekl*gacont_hbr(ll,jj,i)
6934 gradcorr5(ll,m)=gradcorr5(ll,m)+ggg1(ll)
6939 cold gradcorr5(ll,m)=gradcorr5(ll,m)+eel5*eij*gacont_hbr(ll,kk,k)
6940 gradcorr5(ll,m)=gradcorr5(ll,m)+ggg2(ll)
6946 gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,1)
6951 gradcorr5(ll,m)=gradcorr5(ll,m)+ekont*derx(ll,1,2)
6955 cd write (2,*) iii,g_corr5_loc(iii)
6959 cd write (2,*) 'ekont',ekont
6960 cd write (iout,*) 'eello5',ekont*eel5
6963 c--------------------------------------------------------------------------
6964 double precision function eello6(i,j,k,l,jj,kk)
6965 implicit real*8 (a-h,o-z)
6966 include 'DIMENSIONS'
6967 include 'DIMENSIONS.ZSCOPT'
6968 include 'COMMON.IOUNITS'
6969 include 'COMMON.CHAIN'
6970 include 'COMMON.DERIV'
6971 include 'COMMON.INTERACT'
6972 include 'COMMON.CONTACTS'
6973 include 'COMMON.TORSION'
6974 include 'COMMON.VAR'
6975 include 'COMMON.GEO'
6976 include 'COMMON.FFIELD'
6977 double precision ggg1(3),ggg2(3)
6978 cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
6983 cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
6991 cd call checkint6(i,j,k,l,jj,kk,eel6_1_num,eel6_2_num,
6992 cd & eel6_3_num,eel6_4_num,eel6_5_num,eel6_6_num)
6996 derx(lll,kkk,iii)=0.0d0
7000 cd eij=facont_hb(jj,i)
7001 cd ekl=facont_hb(kk,k)
7007 eello6_1=eello6_graph1(i,j,k,l,1,.false.)
7008 eello6_2=eello6_graph1(j,i,l,k,2,.false.)
7009 eello6_3=eello6_graph2(i,j,k,l,jj,kk,.false.)
7010 eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
7011 eello6_5=eello6_graph4(j,i,l,k,jj,kk,2,.false.)
7012 eello6_6=eello6_graph3(i,j,k,l,jj,kk,.false.)
7014 eello6_1=eello6_graph1(i,j,k,l,1,.false.)
7015 eello6_2=eello6_graph1(l,k,j,i,2,.true.)
7016 eello6_3=eello6_graph2(i,l,k,j,jj,kk,.true.)
7017 eello6_4=eello6_graph4(i,j,k,l,jj,kk,1,.false.)
7018 if (wturn6.eq.0.0d0 .or. j.ne.i+4) then
7019 eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
7023 eello6_6=eello6_graph3(i,l,k,j,jj,kk,.true.)
7025 C If turn contributions are considered, they will be handled separately.
7026 eel6=eello6_1+eello6_2+eello6_3+eello6_4+eello6_5+eello6_6
7027 cd write(iout,*) 'eello6_1',eello6_1,' eel6_1_num',16*eel6_1_num
7028 cd write(iout,*) 'eello6_2',eello6_2,' eel6_2_num',16*eel6_2_num
7029 cd write(iout,*) 'eello6_3',eello6_3,' eel6_3_num',16*eel6_3_num
7030 cd write(iout,*) 'eello6_4',eello6_4,' eel6_4_num',16*eel6_4_num
7031 cd write(iout,*) 'eello6_5',eello6_5,' eel6_5_num',16*eel6_5_num
7032 cd write(iout,*) 'eello6_6',eello6_6,' eel6_6_num',16*eel6_6_num
7035 if (j.lt.nres-1) then
7042 if (l.lt.nres-1) then
7050 ggg1(ll)=eel6*g_contij(ll,1)
7051 ggg2(ll)=eel6*g_contij(ll,2)
7052 cold ghalf=0.5d0*eel6*ekl*gacont_hbr(ll,jj,i)
7053 ghalf=0.5d0*ggg1(ll)
7055 gradcorr6(ll,i)=gradcorr6(ll,i)+ghalf+ekont*derx(ll,2,1)
7056 gradcorr6(ll,i+1)=gradcorr6(ll,i+1)+ekont*derx(ll,3,1)
7057 gradcorr6(ll,j)=gradcorr6(ll,j)+ghalf+ekont*derx(ll,4,1)
7058 gradcorr6(ll,j1)=gradcorr6(ll,j1)+ekont*derx(ll,5,1)
7059 ghalf=0.5d0*ggg2(ll)
7060 cold ghalf=0.5d0*eel6*eij*gacont_hbr(ll,kk,k)
7062 gradcorr6(ll,k)=gradcorr6(ll,k)+ghalf+ekont*derx(ll,2,2)
7063 gradcorr6(ll,k+1)=gradcorr6(ll,k+1)+ekont*derx(ll,3,2)
7064 gradcorr6(ll,l)=gradcorr6(ll,l)+ghalf+ekont*derx(ll,4,2)
7065 gradcorr6(ll,l1)=gradcorr6(ll,l1)+ekont*derx(ll,5,2)
7070 cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*ekl*gacont_hbr(ll,jj,i)
7071 gradcorr6(ll,m)=gradcorr6(ll,m)+ggg1(ll)
7076 cold gradcorr6(ll,m)=gradcorr6(ll,m)+eel6*eij*gacont_hbr(ll,kk,k)
7077 gradcorr6(ll,m)=gradcorr6(ll,m)+ggg2(ll)
7083 gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,1)
7088 gradcorr6(ll,m)=gradcorr6(ll,m)+ekont*derx(ll,1,2)
7092 cd write (2,*) iii,g_corr6_loc(iii)
7096 cd write (2,*) 'ekont',ekont
7097 cd write (iout,*) 'eello6',ekont*eel6
7100 c--------------------------------------------------------------------------
7101 double precision function eello6_graph1(i,j,k,l,imat,swap)
7102 implicit real*8 (a-h,o-z)
7103 include 'DIMENSIONS'
7104 include 'DIMENSIONS.ZSCOPT'
7105 include 'COMMON.IOUNITS'
7106 include 'COMMON.CHAIN'
7107 include 'COMMON.DERIV'
7108 include 'COMMON.INTERACT'
7109 include 'COMMON.CONTACTS'
7110 include 'COMMON.TORSION'
7111 include 'COMMON.VAR'
7112 include 'COMMON.GEO'
7113 double precision vv(2),vv1(2),pizda(2,2),auxmat(2,2),pizda1(2,2)
7117 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7119 C Parallel Antiparallel C
7125 C \ j|/k\| / \ |/k\|l / C
7130 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7131 itk=itortyp(itype(k))
7132 s1= scalar2(AEAb1(1,2,imat),CUgb2(1,i))
7133 s2=-scalar2(AEAb2(1,1,imat),Ug2Db1t(1,k))
7134 s3= scalar2(AEAb2(1,1,imat),CUgb2(1,k))
7135 call transpose2(EUgC(1,1,k),auxmat(1,1))
7136 call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
7137 vv1(1)=pizda1(1,1)-pizda1(2,2)
7138 vv1(2)=pizda1(1,2)+pizda1(2,1)
7139 s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
7140 vv(1)=AEAb1(1,2,imat)*b1(1,itk)-AEAb1(2,2,imat)*b1(2,itk)
7141 vv(2)=AEAb1(1,2,imat)*b1(2,itk)+AEAb1(2,2,imat)*b1(1,itk)
7142 s5=scalar2(vv(1),Dtobr2(1,i))
7143 cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4', s4,' s5',s5
7144 eello6_graph1=-0.5d0*(s1+s2+s3+s4+s5)
7145 if (.not. calc_grad) return
7146 if (i.gt.1) g_corr6_loc(i-1)=g_corr6_loc(i-1)
7147 & -0.5d0*ekont*(scalar2(AEAb1(1,2,imat),CUgb2der(1,i))
7148 & -scalar2(AEAb2derg(1,2,1,imat),Ug2Db1t(1,k))
7149 & +scalar2(AEAb2derg(1,2,1,imat),CUgb2(1,k))
7150 & +0.5d0*scalar2(vv1(1),Dtobr2der(1,i))
7151 & +scalar2(vv(1),Dtobr2der(1,i)))
7152 call matmat2(AEAderg(1,1,imat),auxmat(1,1),pizda1(1,1))
7153 vv1(1)=pizda1(1,1)-pizda1(2,2)
7154 vv1(2)=pizda1(1,2)+pizda1(2,1)
7155 vv(1)=AEAb1derg(1,2,imat)*b1(1,itk)-AEAb1derg(2,2,imat)*b1(2,itk)
7156 vv(2)=AEAb1derg(1,2,imat)*b1(2,itk)+AEAb1derg(2,2,imat)*b1(1,itk)
7158 g_corr6_loc(l-1)=g_corr6_loc(l-1)
7159 & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
7160 & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
7161 & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
7162 & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
7164 g_corr6_loc(j-1)=g_corr6_loc(j-1)
7165 & +ekont*(-0.5d0*(scalar2(AEAb1derg(1,2,imat),CUgb2(1,i))
7166 & -scalar2(AEAb2derg(1,1,1,imat),Ug2Db1t(1,k))
7167 & +scalar2(AEAb2derg(1,1,1,imat),CUgb2(1,k))
7168 & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))+scalar2(vv(1),Dtobr2(1,i))))
7170 call transpose2(EUgCder(1,1,k),auxmat(1,1))
7171 call matmat2(AEA(1,1,imat),auxmat(1,1),pizda1(1,1))
7172 vv1(1)=pizda1(1,1)-pizda1(2,2)
7173 vv1(2)=pizda1(1,2)+pizda1(2,1)
7174 if (k.gt.1) g_corr6_loc(k-1)=g_corr6_loc(k-1)
7175 & +ekont*(-0.5d0*(-scalar2(AEAb2(1,1,imat),Ug2Db1tder(1,k))
7176 & +scalar2(AEAb2(1,1,imat),CUgb2der(1,k))
7177 & +0.5d0*scalar2(vv1(1),Dtobr2(1,i))))
7186 s1= scalar2(AEAb1derx(1,lll,kkk,iii,2,imat),CUgb2(1,i))
7187 s2=-scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),Ug2Db1t(1,k))
7188 s3= scalar2(AEAb2derx(1,lll,kkk,iii,1,imat),CUgb2(1,k))
7189 call transpose2(EUgC(1,1,k),auxmat(1,1))
7190 call matmat2(AEAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
7192 vv1(1)=pizda1(1,1)-pizda1(2,2)
7193 vv1(2)=pizda1(1,2)+pizda1(2,1)
7194 s4=0.5d0*scalar2(vv1(1),Dtobr2(1,i))
7195 vv(1)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(1,itk)
7196 & -AEAb1derx(2,lll,kkk,iii,2,imat)*b1(2,itk)
7197 vv(2)=AEAb1derx(1,lll,kkk,iii,2,imat)*b1(2,itk)
7198 & +AEAb1derx(2,lll,kkk,iii,2,imat)*b1(1,itk)
7199 s5=scalar2(vv(1),Dtobr2(1,i))
7200 derx(lll,kkk,ind)=derx(lll,kkk,ind)-0.5d0*(s1+s2+s3+s4+s5)
7206 c----------------------------------------------------------------------------
7207 double precision function eello6_graph2(i,j,k,l,jj,kk,swap)
7208 implicit real*8 (a-h,o-z)
7209 include 'DIMENSIONS'
7210 include 'DIMENSIONS.ZSCOPT'
7211 include 'COMMON.IOUNITS'
7212 include 'COMMON.CHAIN'
7213 include 'COMMON.DERIV'
7214 include 'COMMON.INTERACT'
7215 include 'COMMON.CONTACTS'
7216 include 'COMMON.TORSION'
7217 include 'COMMON.VAR'
7218 include 'COMMON.GEO'
7220 double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
7221 & auxvec1(2),auxvec2(2),auxmat1(2,2)
7224 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7226 C Parallel Antiparallel C
7232 C \ j|/k\| \ |/k\|l C
7237 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7238 cd write (2,*) 'eello6_graph2: i,',i,' j',j,' k',k,' l',l
7239 C AL 7/4/01 s1 would occur in the sixth-order moment,
7240 C but not in a cluster cumulant
7242 s1=dip(1,jj,i)*dip(1,kk,k)
7244 call matvec2(ADtEA1(1,1,1),Ub2(1,k),auxvec(1))
7245 s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
7246 call matvec2(ADtEA(1,1,2),Ub2(1,l),auxvec1(1))
7247 s3=-0.5d0*scalar2(Ub2(1,j),auxvec1(1))
7248 call transpose2(EUg(1,1,k),auxmat(1,1))
7249 call matmat2(ADtEA1(1,1,1),auxmat(1,1),pizda(1,1))
7250 vv(1)=pizda(1,1)-pizda(2,2)
7251 vv(2)=pizda(1,2)+pizda(2,1)
7252 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7253 cd write (2,*) 'eello6_graph2:','s1',s1,' s2',s2,' s3',s3,' s4',s4
7255 eello6_graph2=-(s1+s2+s3+s4)
7257 eello6_graph2=-(s2+s3+s4)
7260 if (.not. calc_grad) return
7261 C Derivatives in gamma(i-1)
7264 s1=dipderg(1,jj,i)*dip(1,kk,k)
7266 s2=-0.5d0*scalar2(Ub2der(1,i),auxvec(1))
7267 call matvec2(ADtEAderg(1,1,1,2),Ub2(1,l),auxvec2(1))
7268 s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
7269 s4=-0.25d0*scalar2(vv(1),Dtobr2der(1,i))
7271 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
7273 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
7275 c g_corr6_loc(i-1)=g_corr6_loc(i-1)-s3
7277 C Derivatives in gamma(k-1)
7279 s1=dip(1,jj,i)*dipderg(1,kk,k)
7281 call matvec2(ADtEA1(1,1,1),Ub2der(1,k),auxvec2(1))
7282 s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
7283 call matvec2(ADtEAderg(1,1,2,2),Ub2(1,l),auxvec2(1))
7284 s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
7285 call transpose2(EUgder(1,1,k),auxmat1(1,1))
7286 call matmat2(ADtEA1(1,1,1),auxmat1(1,1),pizda(1,1))
7287 vv(1)=pizda(1,1)-pizda(2,2)
7288 vv(2)=pizda(1,2)+pizda(2,1)
7289 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7291 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
7293 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
7295 c g_corr6_loc(k-1)=g_corr6_loc(k-1)-s3
7296 C Derivatives in gamma(j-1) or gamma(l-1)
7299 s1=dipderg(3,jj,i)*dip(1,kk,k)
7301 call matvec2(ADtEA1derg(1,1,1,1),Ub2(1,k),auxvec2(1))
7302 s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
7303 s3=-0.5d0*scalar2(Ub2der(1,j),auxvec1(1))
7304 call matmat2(ADtEA1derg(1,1,1,1),auxmat(1,1),pizda(1,1))
7305 vv(1)=pizda(1,1)-pizda(2,2)
7306 vv(2)=pizda(1,2)+pizda(2,1)
7307 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7310 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
7312 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
7315 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s3+s4)
7316 c g_corr6_loc(j-1)=g_corr6_loc(j-1)-s3
7318 C Derivatives in gamma(l-1) or gamma(j-1)
7321 s1=dip(1,jj,i)*dipderg(3,kk,k)
7323 call matvec2(ADtEA1derg(1,1,2,1),Ub2(1,k),auxvec2(1))
7324 s2=-0.5d0*scalar2(Ub2(1,i),auxvec2(1))
7325 call matvec2(ADtEA(1,1,2),Ub2der(1,l),auxvec2(1))
7326 s3=-0.5d0*scalar2(Ub2(1,j),auxvec2(1))
7327 call matmat2(ADtEA1derg(1,1,2,1),auxmat(1,1),pizda(1,1))
7328 vv(1)=pizda(1,1)-pizda(2,2)
7329 vv(2)=pizda(1,2)+pizda(2,1)
7330 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7333 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*s1
7335 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*s1
7338 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s3+s4)
7339 c g_corr6_loc(l-1)=g_corr6_loc(l-1)-s3
7341 C Cartesian derivatives.
7343 write (2,*) 'In eello6_graph2'
7345 write (2,*) 'iii=',iii
7347 write (2,*) 'kkk=',kkk
7349 write (2,'(3(2f10.5),5x)')
7350 & ((ADtEA1derx(jjj,mmm,lll,kkk,iii,1),mmm=1,2),lll=1,3)
7360 s1=dipderx(lll,kkk,1,jj,i)*dip(1,kk,k)
7362 s1=dip(1,jj,i)*dipderx(lll,kkk,1,kk,k)
7365 call matvec2(ADtEA1derx(1,1,lll,kkk,iii,1),Ub2(1,k),
7367 s2=-0.5d0*scalar2(Ub2(1,i),auxvec(1))
7368 call matvec2(ADtEAderx(1,1,lll,kkk,iii,2),Ub2(1,l),
7370 s3=-0.5d0*scalar2(Ub2(1,j),auxvec(1))
7371 call transpose2(EUg(1,1,k),auxmat(1,1))
7372 call matmat2(ADtEA1derx(1,1,lll,kkk,iii,1),auxmat(1,1),
7374 vv(1)=pizda(1,1)-pizda(2,2)
7375 vv(2)=pizda(1,2)+pizda(2,1)
7376 s4=-0.25d0*scalar2(vv(1),Dtobr2(1,i))
7377 cd write (2,*) 's1',s1,' s2',s2,' s3',s3,' s4',s4
7379 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
7381 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
7384 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
7386 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7393 c----------------------------------------------------------------------------
7394 double precision function eello6_graph3(i,j,k,l,jj,kk,swap)
7395 implicit real*8 (a-h,o-z)
7396 include 'DIMENSIONS'
7397 include 'DIMENSIONS.ZSCOPT'
7398 include 'COMMON.IOUNITS'
7399 include 'COMMON.CHAIN'
7400 include 'COMMON.DERIV'
7401 include 'COMMON.INTERACT'
7402 include 'COMMON.CONTACTS'
7403 include 'COMMON.TORSION'
7404 include 'COMMON.VAR'
7405 include 'COMMON.GEO'
7406 double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2)
7408 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7410 C Parallel Antiparallel C
7416 C j|/k\| / |/k\|l / C
7421 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7423 C 4/7/01 AL Component s1 was removed, because it pertains to the respective
7424 C energy moment and not to the cluster cumulant.
7425 iti=itortyp(itype(i))
7426 if (j.lt.nres-1) then
7427 itj1=itortyp(itype(j+1))
7431 itk=itortyp(itype(k))
7432 itk1=itortyp(itype(k+1))
7433 if (l.lt.nres-1) then
7434 itl1=itortyp(itype(l+1))
7439 s1=dip(4,jj,i)*dip(4,kk,k)
7441 call matvec2(AECA(1,1,1),b1(1,itk1),auxvec(1))
7442 s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
7443 call matvec2(AECA(1,1,2),b1(1,itl1),auxvec(1))
7444 s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
7445 call transpose2(EE(1,1,itk),auxmat(1,1))
7446 call matmat2(auxmat(1,1),AECA(1,1,1),pizda(1,1))
7447 vv(1)=pizda(1,1)+pizda(2,2)
7448 vv(2)=pizda(2,1)-pizda(1,2)
7449 s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
7450 cd write (2,*) 'eello6_graph3:','s1',s1,' s2',s2,' s3',s3,' s4',s4
7452 eello6_graph3=-(s1+s2+s3+s4)
7454 eello6_graph3=-(s2+s3+s4)
7457 if (.not. calc_grad) return
7458 C Derivatives in gamma(k-1)
7459 call matvec2(AECAderg(1,1,2),b1(1,itl1),auxvec(1))
7460 s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
7461 s4=-0.25d0*scalar2(vv(1),Ctobrder(1,k))
7462 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s3+s4)
7463 C Derivatives in gamma(l-1)
7464 call matvec2(AECAderg(1,1,1),b1(1,itk1),auxvec(1))
7465 s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
7466 call matmat2(auxmat(1,1),AECAderg(1,1,1),pizda(1,1))
7467 vv(1)=pizda(1,1)+pizda(2,2)
7468 vv(2)=pizda(2,1)-pizda(1,2)
7469 s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
7470 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
7471 C Cartesian derivatives.
7477 s1=dipderx(lll,kkk,4,jj,i)*dip(4,kk,k)
7479 s1=dip(4,jj,i)*dipderx(lll,kkk,4,kk,k)
7482 call matvec2(AECAderx(1,1,lll,kkk,iii,1),b1(1,itk1),
7484 s2=0.5d0*scalar2(b1(1,itk),auxvec(1))
7485 call matvec2(AECAderx(1,1,lll,kkk,iii,2),b1(1,itl1),
7487 s3=0.5d0*scalar2(b1(1,itj1),auxvec(1))
7488 call matmat2(auxmat(1,1),AECAderx(1,1,lll,kkk,iii,1),
7490 vv(1)=pizda(1,1)+pizda(2,2)
7491 vv(2)=pizda(2,1)-pizda(1,2)
7492 s4=-0.25d0*scalar2(vv(1),Ctobr(1,k))
7494 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
7496 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
7499 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
7501 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7503 c derx(lll,kkk,iii)=derx(lll,kkk,iii)-s4
7509 c----------------------------------------------------------------------------
7510 double precision function eello6_graph4(i,j,k,l,jj,kk,imat,swap)
7511 implicit real*8 (a-h,o-z)
7512 include 'DIMENSIONS'
7513 include 'DIMENSIONS.ZSCOPT'
7514 include 'COMMON.IOUNITS'
7515 include 'COMMON.CHAIN'
7516 include 'COMMON.DERIV'
7517 include 'COMMON.INTERACT'
7518 include 'COMMON.CONTACTS'
7519 include 'COMMON.TORSION'
7520 include 'COMMON.VAR'
7521 include 'COMMON.GEO'
7522 include 'COMMON.FFIELD'
7523 double precision vv(2),pizda(2,2),auxmat(2,2),auxvec(2),
7524 & auxvec1(2),auxmat1(2,2)
7526 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7528 C Parallel Antiparallel C
7534 C \ j|/k\| \ |/k\|l C
7539 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
7541 C 4/7/01 AL Component s1 was removed, because it pertains to the respective
7542 C energy moment and not to the cluster cumulant.
7543 cd write (2,*) 'eello_graph4: wturn6',wturn6
7544 iti=itortyp(itype(i))
7545 itj=itortyp(itype(j))
7546 if (j.lt.nres-1) then
7547 itj1=itortyp(itype(j+1))
7551 itk=itortyp(itype(k))
7552 if (k.lt.nres-1) then
7553 itk1=itortyp(itype(k+1))
7557 itl=itortyp(itype(l))
7558 if (l.lt.nres-1) then
7559 itl1=itortyp(itype(l+1))
7563 cd write (2,*) 'eello6_graph4:','i',i,' j',j,' k',k,' l',l
7564 cd write (2,*) 'iti',iti,' itj',itj,' itj1',itj1,' itk',itk,
7565 cd & ' itl',itl,' itl1',itl1
7568 s1=dip(3,jj,i)*dip(3,kk,k)
7570 s1=dip(2,jj,j)*dip(2,kk,l)
7573 call matvec2(AECA(1,1,imat),Ub2(1,k),auxvec(1))
7574 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7576 call matvec2(ADtEA1(1,1,3-imat),b1(1,itj1),auxvec1(1))
7577 s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
7579 call matvec2(ADtEA1(1,1,3-imat),b1(1,itl1),auxvec1(1))
7580 s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
7582 call transpose2(EUg(1,1,k),auxmat(1,1))
7583 call matmat2(AECA(1,1,imat),auxmat(1,1),pizda(1,1))
7584 vv(1)=pizda(1,1)-pizda(2,2)
7585 vv(2)=pizda(2,1)+pizda(1,2)
7586 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7587 cd write (2,*) 'eello6_graph4:','s1',s1,' s2',s2,' s3',s3,' s4',s4
7589 eello6_graph4=-(s1+s2+s3+s4)
7591 eello6_graph4=-(s2+s3+s4)
7593 if (.not. calc_grad) return
7594 C Derivatives in gamma(i-1)
7598 s1=dipderg(2,jj,i)*dip(3,kk,k)
7600 s1=dipderg(4,jj,j)*dip(2,kk,l)
7603 s2=0.5d0*scalar2(Ub2der(1,i),auxvec(1))
7605 call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itj1),auxvec1(1))
7606 s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
7608 call matvec2(ADtEA1derg(1,1,1,3-imat),b1(1,itl1),auxvec1(1))
7609 s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
7611 s4=0.25d0*scalar2(vv(1),Dtobr2der(1,i))
7612 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7613 cd write (2,*) 'turn6 derivatives'
7615 gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s1+s2+s3+s4)
7617 gel_loc_turn6(i-1)=gel_loc_turn6(i-1)-ekont*(s2+s3+s4)
7621 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s1+s2+s3+s4)
7623 g_corr6_loc(i-1)=g_corr6_loc(i-1)-ekont*(s2+s3+s4)
7627 C Derivatives in gamma(k-1)
7630 s1=dip(3,jj,i)*dipderg(2,kk,k)
7632 s1=dip(2,jj,j)*dipderg(4,kk,l)
7635 call matvec2(AECA(1,1,imat),Ub2der(1,k),auxvec1(1))
7636 s2=0.5d0*scalar2(Ub2(1,i),auxvec1(1))
7638 call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itj1),auxvec1(1))
7639 s3=-0.5d0*scalar2(b1(1,itj),auxvec1(1))
7641 call matvec2(ADtEA1derg(1,1,2,3-imat),b1(1,itl1),auxvec1(1))
7642 s3=-0.5d0*scalar2(b1(1,itl),auxvec1(1))
7644 call transpose2(EUgder(1,1,k),auxmat1(1,1))
7645 call matmat2(AECA(1,1,imat),auxmat1(1,1),pizda(1,1))
7646 vv(1)=pizda(1,1)-pizda(2,2)
7647 vv(2)=pizda(2,1)+pizda(1,2)
7648 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7649 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7651 gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s1+s2+s3+s4)
7653 gel_loc_turn6(k-1)=gel_loc_turn6(k-1)-ekont*(s2+s3+s4)
7657 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s1+s2+s3+s4)
7659 g_corr6_loc(k-1)=g_corr6_loc(k-1)-ekont*(s2+s3+s4)
7662 C Derivatives in gamma(j-1) or gamma(l-1)
7663 if (l.eq.j+1 .and. l.gt.1) then
7664 call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
7665 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7666 call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
7667 vv(1)=pizda(1,1)-pizda(2,2)
7668 vv(2)=pizda(2,1)+pizda(1,2)
7669 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7670 g_corr6_loc(l-1)=g_corr6_loc(l-1)-ekont*(s2+s4)
7671 else if (j.gt.1) then
7672 call matvec2(AECAderg(1,1,imat),Ub2(1,k),auxvec(1))
7673 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7674 call matmat2(AECAderg(1,1,imat),auxmat(1,1),pizda(1,1))
7675 vv(1)=pizda(1,1)-pizda(2,2)
7676 vv(2)=pizda(2,1)+pizda(1,2)
7677 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7678 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7679 gel_loc_turn6(j-1)=gel_loc_turn6(j-1)-ekont*(s2+s4)
7681 g_corr6_loc(j-1)=g_corr6_loc(j-1)-ekont*(s2+s4)
7684 C Cartesian derivatives.
7691 s1=dipderx(lll,kkk,3,jj,i)*dip(3,kk,k)
7693 s1=dipderx(lll,kkk,2,jj,j)*dip(2,kk,l)
7697 s1=dip(3,jj,i)*dipderx(lll,kkk,3,kk,k)
7699 s1=dip(2,jj,j)*dipderx(lll,kkk,2,kk,l)
7703 call matvec2(AECAderx(1,1,lll,kkk,iii,imat),Ub2(1,k),
7705 s2=0.5d0*scalar2(Ub2(1,i),auxvec(1))
7707 call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
7708 & b1(1,itj1),auxvec(1))
7709 s3=-0.5d0*scalar2(b1(1,itj),auxvec(1))
7711 call matvec2(ADtEA1derx(1,1,lll,kkk,iii,3-imat),
7712 & b1(1,itl1),auxvec(1))
7713 s3=-0.5d0*scalar2(b1(1,itl),auxvec(1))
7715 call matmat2(AECAderx(1,1,lll,kkk,iii,imat),auxmat(1,1),
7717 vv(1)=pizda(1,1)-pizda(2,2)
7718 vv(2)=pizda(2,1)+pizda(1,2)
7719 s4=0.25d0*scalar2(vv(1),Dtobr2(1,i))
7721 if (wturn6.gt.0.0d0 .and. k.eq.l+4 .and. i.eq.j+2) then
7723 derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
7726 derx_turn(lll,kkk,3-iii)=derx_turn(lll,kkk,3-iii)
7729 derx_turn(lll,kkk,iii)=derx_turn(lll,kkk,iii)-s3
7732 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s1+s2+s4)
7734 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-(s2+s4)
7736 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7740 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s1+s2+s4)
7742 derx(lll,kkk,iii)=derx(lll,kkk,iii)-(s2+s4)
7745 derx(lll,kkk,iii)=derx(lll,kkk,iii)-s3
7747 derx(lll,kkk,3-iii)=derx(lll,kkk,3-iii)-s3
7755 c----------------------------------------------------------------------------
7756 double precision function eello_turn6(i,jj,kk)
7757 implicit real*8 (a-h,o-z)
7758 include 'DIMENSIONS'
7759 include 'DIMENSIONS.ZSCOPT'
7760 include 'COMMON.IOUNITS'
7761 include 'COMMON.CHAIN'
7762 include 'COMMON.DERIV'
7763 include 'COMMON.INTERACT'
7764 include 'COMMON.CONTACTS'
7765 include 'COMMON.TORSION'
7766 include 'COMMON.VAR'
7767 include 'COMMON.GEO'
7768 double precision vtemp1(2),vtemp2(2),vtemp3(2),vtemp4(2),
7769 & atemp(2,2),auxmat(2,2),achuj_temp(2,2),gtemp(2,2),gvec(2),
7771 double precision vtemp1d(2),vtemp2d(2),vtemp3d(2),vtemp4d(2),
7772 & atempd(2,2),auxmatd(2,2),achuj_tempd(2,2),gtempd(2,2),gvecd(2)
7773 C 4/7/01 AL Components s1, s8, and s13 were removed, because they pertain to
7774 C the respective energy moment and not to the cluster cumulant.
7779 iti=itortyp(itype(i))
7780 itk=itortyp(itype(k))
7781 itk1=itortyp(itype(k+1))
7782 itl=itortyp(itype(l))
7783 itj=itortyp(itype(j))
7784 cd write (2,*) 'itk',itk,' itk1',itk1,' itl',itl,' itj',itj
7785 cd write (2,*) 'i',i,' k',k,' j',j,' l',l
7786 cd if (i.ne.1 .or. j.ne.3 .or. k.ne.2 .or. l.ne.4) then
7791 cd & 'EELLO6: Contacts have occurred for peptide groups',i,j,
7793 cd call checkint_turn6(i,jj,kk,eel_turn6_num)
7797 derx_turn(lll,kkk,iii)=0.0d0
7804 eello6_5=eello6_graph4(l,k,j,i,kk,jj,2,.true.)
7806 cd write (2,*) 'eello6_5',eello6_5
7808 call transpose2(AEA(1,1,1),auxmat(1,1))
7809 call matmat2(EUg(1,1,i+1),auxmat(1,1),auxmat(1,1))
7810 ss1=scalar2(Ub2(1,i+2),b1(1,itl))
7811 s1 = (auxmat(1,1)+auxmat(2,2))*ss1
7815 call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
7816 call matvec2(AEA(1,1,1),vtemp1(1),vtemp1(1))
7817 s2 = scalar2(b1(1,itk),vtemp1(1))
7819 call transpose2(AEA(1,1,2),atemp(1,1))
7820 call matmat2(atemp(1,1),EUg(1,1,i+4),atemp(1,1))
7821 call matvec2(Ug2(1,1,i+2),dd(1,1,itk1),vtemp2(1))
7822 s8 = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
7826 call matmat2(EUg(1,1,i+3),AEA(1,1,2),auxmat(1,1))
7827 call matvec2(auxmat(1,1),Ub2(1,i+4),vtemp3(1))
7828 s12 = scalar2(Ub2(1,i+2),vtemp3(1))
7830 call transpose2(a_chuj(1,1,kk,i+1),achuj_temp(1,1))
7831 call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtemp(1,1))
7832 call matmat2(gtemp(1,1),EUg(1,1,i+3),gtemp(1,1))
7833 call matvec2(a_chuj(1,1,jj,i),Ub2(1,i+4),vtemp4(1))
7834 ss13 = scalar2(b1(1,itk),vtemp4(1))
7835 s13 = (gtemp(1,1)+gtemp(2,2))*ss13
7839 c write (2,*) 's1,s2,s8,s12,s13',s1,s2,s8,s12,s13
7845 eel_turn6 = eello6_5 - 0.5d0*(s1+s2+s12+s8+s13)
7847 C Derivatives in gamma(i+2)
7849 call transpose2(AEA(1,1,1),auxmatd(1,1))
7850 call matmat2(EUgder(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7851 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
7852 call transpose2(AEAderg(1,1,2),atempd(1,1))
7853 call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
7854 s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
7858 call matmat2(EUg(1,1,i+3),AEAderg(1,1,2),auxmatd(1,1))
7859 call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
7860 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7866 gel_loc_turn6(i)=gel_loc_turn6(i)-0.5d0*ekont*(s1d+s8d+s12d)
7867 C Derivatives in gamma(i+3)
7869 call transpose2(AEA(1,1,1),auxmatd(1,1))
7870 call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7871 ss1d=scalar2(Ub2der(1,i+2),b1(1,itl))
7872 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1d
7876 call matvec2(EUgder(1,1,i+2),b1(1,itl),vtemp1d(1))
7877 call matvec2(AEA(1,1,1),vtemp1d(1),vtemp1d(1))
7878 s2d = scalar2(b1(1,itk),vtemp1d(1))
7880 call matvec2(Ug2der(1,1,i+2),dd(1,1,itk1),vtemp2d(1))
7881 s8d = -(atemp(1,1)+atemp(2,2))*scalar2(cc(1,1,itl),vtemp2d(1))
7883 s12d = scalar2(Ub2der(1,i+2),vtemp3(1))
7885 call matmat2(achuj_temp(1,1),EUgder(1,1,i+2),gtempd(1,1))
7886 call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
7887 s13d = (gtempd(1,1)+gtempd(2,2))*ss13
7897 gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
7898 & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
7900 gel_loc_turn6(i+1)=gel_loc_turn6(i+1)
7901 & -0.5d0*ekont*(s2d+s12d)
7903 C Derivatives in gamma(i+4)
7904 call matmat2(EUgder(1,1,i+3),AEA(1,1,2),auxmatd(1,1))
7905 call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
7906 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7908 call matmat2(achuj_temp(1,1),EUg(1,1,i+2),gtempd(1,1))
7909 call matmat2(gtempd(1,1),EUgder(1,1,i+3),gtempd(1,1))
7910 s13d = (gtempd(1,1)+gtempd(2,2))*ss13
7920 gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d+s13d)
7922 gel_loc_turn6(i+2)=gel_loc_turn6(i+2)-0.5d0*ekont*(s12d)
7924 C Derivatives in gamma(i+5)
7926 call transpose2(AEAderg(1,1,1),auxmatd(1,1))
7927 call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7928 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
7932 call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1d(1))
7933 call matvec2(AEAderg(1,1,1),vtemp1d(1),vtemp1d(1))
7934 s2d = scalar2(b1(1,itk),vtemp1d(1))
7936 call transpose2(AEA(1,1,2),atempd(1,1))
7937 call matmat2(atempd(1,1),EUgder(1,1,i+4),atempd(1,1))
7938 s8d = -(atempd(1,1)+atempd(2,2))*scalar2(cc(1,1,itl),vtemp2(1))
7942 call matvec2(auxmat(1,1),Ub2der(1,i+4),vtemp3d(1))
7943 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7945 call matvec2(a_chuj(1,1,jj,i),Ub2der(1,i+4),vtemp4d(1))
7946 ss13d = scalar2(b1(1,itk),vtemp4d(1))
7947 s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
7957 gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
7958 & -0.5d0*ekont*(s1d+s2d+s8d+s12d+s13d)
7960 gel_loc_turn6(i+3)=gel_loc_turn6(i+3)
7961 & -0.5d0*ekont*(s2d+s12d)
7963 C Cartesian derivatives
7968 call transpose2(AEAderx(1,1,lll,kkk,iii,1),auxmatd(1,1))
7969 call matmat2(EUg(1,1,i+1),auxmatd(1,1),auxmatd(1,1))
7970 s1d = (auxmatd(1,1)+auxmatd(2,2))*ss1
7974 call matvec2(EUg(1,1,i+2),b1(1,itl),vtemp1(1))
7975 call matvec2(AEAderx(1,1,lll,kkk,iii,1),vtemp1(1),
7977 s2d = scalar2(b1(1,itk),vtemp1d(1))
7979 call transpose2(AEAderx(1,1,lll,kkk,iii,2),atempd(1,1))
7980 call matmat2(atempd(1,1),EUg(1,1,i+4),atempd(1,1))
7981 s8d = -(atempd(1,1)+atempd(2,2))*
7982 & scalar2(cc(1,1,itl),vtemp2(1))
7986 call matmat2(EUg(1,1,i+3),AEAderx(1,1,lll,kkk,iii,2),
7988 call matvec2(auxmatd(1,1),Ub2(1,i+4),vtemp3d(1))
7989 s12d = scalar2(Ub2(1,i+2),vtemp3d(1))
7996 derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
7999 derx_turn(lll,kkk,iii) = derx_turn(lll,kkk,iii)
8003 derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
8004 & - 0.5d0*(s8d+s12d)
8006 derx_turn(lll,kkk,3-iii) = derx_turn(lll,kkk,3-iii)
8015 call transpose2(a_chuj_der(1,1,lll,kkk,kk,i+1),
8017 call matmat2(achuj_tempd(1,1),EUg(1,1,i+2),gtempd(1,1))
8018 call matmat2(gtempd(1,1),EUg(1,1,i+3),gtempd(1,1))
8019 s13d=(gtempd(1,1)+gtempd(2,2))*ss13
8020 derx_turn(lll,kkk,2) = derx_turn(lll,kkk,2)-0.5d0*s13d
8021 call matvec2(a_chuj_der(1,1,lll,kkk,jj,i),Ub2(1,i+4),
8023 ss13d = scalar2(b1(1,itk),vtemp4d(1))
8024 s13d = (gtemp(1,1)+gtemp(2,2))*ss13d
8025 derx_turn(lll,kkk,1) = derx_turn(lll,kkk,1)-0.5d0*s13d
8029 cd write(iout,*) 'eel6_turn6',eel_turn6,' eel_turn6_num',
8030 cd & 16*eel_turn6_num
8032 if (j.lt.nres-1) then
8039 if (l.lt.nres-1) then
8047 ggg1(ll)=eel_turn6*g_contij(ll,1)
8048 ggg2(ll)=eel_turn6*g_contij(ll,2)
8049 ghalf=0.5d0*ggg1(ll)
8051 gcorr6_turn(ll,i)=gcorr6_turn(ll,i)+ghalf
8052 & +ekont*derx_turn(ll,2,1)
8053 gcorr6_turn(ll,i+1)=gcorr6_turn(ll,i+1)+ekont*derx_turn(ll,3,1)
8054 gcorr6_turn(ll,j)=gcorr6_turn(ll,j)+ghalf
8055 & +ekont*derx_turn(ll,4,1)
8056 gcorr6_turn(ll,j1)=gcorr6_turn(ll,j1)+ekont*derx_turn(ll,5,1)
8057 ghalf=0.5d0*ggg2(ll)
8059 gcorr6_turn(ll,k)=gcorr6_turn(ll,k)+ghalf
8060 & +ekont*derx_turn(ll,2,2)
8061 gcorr6_turn(ll,k+1)=gcorr6_turn(ll,k+1)+ekont*derx_turn(ll,3,2)
8062 gcorr6_turn(ll,l)=gcorr6_turn(ll,l)+ghalf
8063 & +ekont*derx_turn(ll,4,2)
8064 gcorr6_turn(ll,l1)=gcorr6_turn(ll,l1)+ekont*derx_turn(ll,5,2)
8069 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg1(ll)
8074 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ggg2(ll)
8080 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,1)
8085 gcorr6_turn(ll,m)=gcorr6_turn(ll,m)+ekont*derx_turn(ll,1,2)
8089 cd write (2,*) iii,g_corr6_loc(iii)
8092 eello_turn6=ekont*eel_turn6
8093 cd write (2,*) 'ekont',ekont
8094 cd write (2,*) 'eel_turn6',ekont*eel_turn6
8097 crc-------------------------------------------------
8098 SUBROUTINE MATVEC2(A1,V1,V2)
8099 implicit real*8 (a-h,o-z)
8100 include 'DIMENSIONS'
8101 DIMENSION A1(2,2),V1(2),V2(2)
8105 c 3 VI=VI+A1(I,K)*V1(K)
8109 vaux1=a1(1,1)*v1(1)+a1(1,2)*v1(2)
8110 vaux2=a1(2,1)*v1(1)+a1(2,2)*v1(2)
8115 C---------------------------------------
8116 SUBROUTINE MATMAT2(A1,A2,A3)
8117 implicit real*8 (a-h,o-z)
8118 include 'DIMENSIONS'
8119 DIMENSION A1(2,2),A2(2,2),A3(2,2)
8120 c DIMENSION AI3(2,2)
8124 c A3IJ=A3IJ+A1(I,K)*A2(K,J)
8130 ai3_11=a1(1,1)*a2(1,1)+a1(1,2)*a2(2,1)
8131 ai3_12=a1(1,1)*a2(1,2)+a1(1,2)*a2(2,2)
8132 ai3_21=a1(2,1)*a2(1,1)+a1(2,2)*a2(2,1)
8133 ai3_22=a1(2,1)*a2(1,2)+a1(2,2)*a2(2,2)
8141 c-------------------------------------------------------------------------
8142 double precision function scalar2(u,v)
8144 double precision u(2),v(2)
8147 scalar2=u(1)*v(1)+u(2)*v(2)
8151 C-----------------------------------------------------------------------------
8153 subroutine transpose2(a,at)
8155 double precision a(2,2),at(2,2)
8162 c--------------------------------------------------------------------------
8163 subroutine transpose(n,a,at)
8166 double precision a(n,n),at(n,n)
8174 C---------------------------------------------------------------------------
8175 subroutine prodmat3(a1,a2,kk,transp,prod)
8178 double precision a1(2,2),a2(2,2),a2t(2,2),kk(2,2),prod(2,2)
8180 crc double precision auxmat(2,2),prod_(2,2)
8183 crc call transpose2(kk(1,1),auxmat(1,1))
8184 crc call matmat2(a1(1,1),auxmat(1,1),auxmat(1,1))
8185 crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
8187 prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,1)
8188 & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,1)
8189 prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(1,2))*a2(1,2)
8190 & +(a1(1,1)*kk(2,1)+a1(1,2)*kk(2,2))*a2(2,2)
8191 prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,1)
8192 & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,1)
8193 prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(1,2))*a2(1,2)
8194 & +(a1(2,1)*kk(2,1)+a1(2,2)*kk(2,2))*a2(2,2)
8197 crc call matmat2(a1(1,1),kk(1,1),auxmat(1,1))
8198 crc call matmat2(auxmat(1,1),a2(1,1),prod_(1,1))
8200 prod(1,1)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,1)
8201 & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,1)
8202 prod(1,2)=(a1(1,1)*kk(1,1)+a1(1,2)*kk(2,1))*a2(1,2)
8203 & +(a1(1,1)*kk(1,2)+a1(1,2)*kk(2,2))*a2(2,2)
8204 prod(2,1)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,1)
8205 & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,1)
8206 prod(2,2)=(a1(2,1)*kk(1,1)+a1(2,2)*kk(2,1))*a2(1,2)
8207 & +(a1(2,1)*kk(1,2)+a1(2,2)*kk(2,2))*a2(2,2)
8210 c call transpose2(a2(1,1),a2t(1,1))
8213 crc print *,((prod_(i,j),i=1,2),j=1,2)
8214 crc print *,((prod(i,j),i=1,2),j=1,2)
8218 C-----------------------------------------------------------------------------
8219 double precision function scalar(u,v)
8221 double precision u(3),v(3)