2 !-----------------------------------------------------------------------------
4 !-----------------------------------------------------------------------------
5 ! Max. number of energy intervals
6 integer,parameter :: max_ene=57 !10
7 !-----------------------------------------------------------------------------
8 ! Maximum number of terms in SC bond-stretching potential
9 integer,parameter :: maxbondterm=3
10 !-----------------------------------------------------------------------------
11 ! Max. number of derivatives of virtual-bond and side-chain vectors in theta
14 !-----------------------------------------------------------------------------
15 ! Max. number of contacts per residue
17 integer,parameter :: maxcontsshi=50
18 !-----------------------------------------------------------------------------
19 ! Max. number of SC contacts
21 ! Maximum number of valence and torsional in rigorous approach
22 integer,parameter :: maxtor_kcc=6
23 integer,parameter :: maxval_kcc=6
24 integer,parameter :: maxang_kcc=36
26 !-----------------------------------------------------------------------------
29 integer :: ncont,ncont_ref
30 integer,dimension(:,:),allocatable :: icont,icont_ref !(2,maxcont)
32 ! integer,dimension(:),allocatable :: nsccont_frag_ref !(mmaxfrag) !wham
33 ! integer,dimension(:,:,:),allocatable :: isccont_frag_ref !(2,maxcont,mmaxfrag) !wham
35 ! 12/13/2008 (again Poland-Jaruzel war anniversary)
36 ! RE: Parallelization of 4th and higher order loc-el correlations
37 ! common /contdistrib/
38 integer,dimension(:),allocatable :: iat_sent !(maxres)
39 ! iat_sent - zainicjowane w initialize_p.F;
40 integer,dimension(:,:,:),allocatable :: iint_sent,iint_sent_local !(4,maxres,maxres)
41 integer,dimension(:,:),allocatable :: iturn3_sent,iturn4_sent,&
42 iturn3_sent_local,iturn4_sent_local !(4,maxres),
43 integer,dimension(:),allocatable :: itask_cont_from,itask_cont_to !(0:max_fg_procs-1),
44 integer :: nat_sent,ntask_cont_from,ntask_cont_to
45 !-----------------------------------------------------------------------------
48 real(kind=8),dimension(:,:),allocatable :: dcdv,dxdv !(6,maxdim)
49 real(kind=8),dimension(:,:),allocatable :: dxds !(6,maxres)
50 real(kind=8),dimension(:,:,:),allocatable :: gradx,gradc !(3,maxres,2)
51 real(kind=8),dimension(:,:),allocatable :: gvdwx !(3,maxres)
52 real(kind=8),dimension(:,:),allocatable :: gloc,gloc_x !(maxvar,2) ,gloc_x !!! nie używane
53 real(kind=8),dimension(:,:,:),allocatable :: dtheta !(3,2,maxres)
54 real(kind=8),dimension(:,:,:),allocatable :: dphi,dalpha,domega !(3,3,maxres)
57 ! common /derivat/ wham
60 integer :: igrad_start,igrad_end
61 integer,dimension(:),allocatable :: jgrad_start,jgrad_end !(maxres)
62 !-----------------------------------------------------------------------------
63 ! The following COMMON block selects the type of the force field used in
64 ! calculations and defines weights of various energy terms.
66 !-----------------------------------------------------------------------------
70 integer :: rescale_mode
71 real(kind=8) :: wsc,wscp,welec,wbond,wstrain,wtor,wtor_d,wang,&
72 wscloc,wcorr,wcorr4,wcorr5,wcorr6,wsccor,wel_loc,wturn3,wturn4,&
73 wturn6,wvdwpp,wliptran,wshield,lipscale,wtube, &
74 wbond_nucl,wang_nucl,wcorr_nucl,wcorr3_nucl,welpp,wtor_nucl,&
75 wtor_d_nucl,welsb,wsbloc,wvdwsb,welpsb,wvdwpp_nucl,wvdwpsb,wcatprot,&
76 wcatcat,wscbase,wpepbase,wscpho,wpeppho,wdihc,wcatnucl,wcat_tran,wcat_ang,&
79 real(kind=8) :: scalscp
81 real(kind=8),dimension(:),allocatable :: weights !(n_ene)
82 real(kind=8) :: temp0,scal14,cutoff_corr,delt_corr,r0_corr
83 integer :: ipot,ipot_nucl
85 character(len=3),dimension(5) :: potname = &
86 (/'LJ ','LJK','BP ','GB ','GBV'/)
87 !-----------------------------------------------------------------------------
88 ! wlong,welec,wtor,wang,wscloc are the weight of the energy terms
89 ! corresponding to side-chain, electrostatic, torsional, valence-angle,
90 ! and local side-chain terms.
92 ! IPOT determines which SC...SC interaction potential will be used:
93 ! 1 - LJ: 2n-n Lennard-Jones
94 ! 2 - LJK: 2n-n Kihara type (shifted Lennard-Jones)
95 ! 3 - BP; Berne-Pechukas (angular dependence)
96 ! 4 - GB; Gay-Berne (angular dependence)
97 ! 5 - GBV; Gay-Berne-Vorobjev; angularly-dependent Kihara potential
98 !-----------------------------------------------------------------------------
101 real(kind=8),dimension(:,:),allocatable :: aa_aq,bb_aq,augm,aa_lip,bb_lip !(ntyp,ntyp)
102 real(kind=8),dimension(:),allocatable :: sc_aa_tube_par,sc_bb_tube_par,&
103 acavtub,bcavtub,ccavtub,dcavtub,tubetranene
104 real(kind=8),dimension(:,:),allocatable :: aa_nucl,bb_nucl
105 real(kind=8) :: acavtubpep,bcavtubpep,ccavtubpep,dcavtubpep, &
106 tubetranenepep,pep_aa_tube,pep_bb_tube,tubeR0
107 real(kind=8),dimension(3) :: tubecenter
108 real(kind=8),dimension(:,:),allocatable :: aad,bad !(ntyp,2)
109 real(kind=8),dimension(2,2) :: app,bpp,ael6,ael3
110 real(kind=8),dimension(:),allocatable :: aad_nucl,bad_nucl !(ntyp,2)
111 real(kind=8),dimension(2,2) :: app_nucl,bpp_nucl
112 real(kind=8),dimension(:,:),allocatable :: ael6_nucl,&
113 ael3_nucl,ael32_nucl,ael63_nucl
114 integer :: expon,expon2, nnt,nct,itypro
115 integer,dimension(5) :: nnt_molec,nct_molec
116 integer,dimension(:,:),allocatable :: istart,iend !(maxres,maxint_gr)
117 integer,dimension(:),allocatable :: nint_gr,itel,&
118 ielstart,ielend,ielstart_vdw,ielend_vdw,nscp_gr !(maxres)
119 integer,dimension(:,:),allocatable :: istart_nucl,iend_nucl !(maxres,maxint_gr)
120 integer,dimension(:),allocatable :: nint_gr_nucl,itel_nucl,&
121 ielstart_nucl,ielend_nucl,ielstart_vdw_nucl,ielend_vdw_nucl,nscp_gr_nucl !(maxres)
122 integer,dimension(:,:),allocatable :: iscpstart_nucl,iscpend_nucl !(maxres,maxint_gr)
124 integer,dimension(:),allocatable :: istype,molnum
125 integer,dimension(:,:),allocatable :: itype ! now itype has more molecule types
126 integer,dimension(:,:),allocatable :: iscpstart,iscpend !(maxres,maxint_gr)
127 integer :: iatsc_s,iatsc_e,iatel_s,iatel_e,iatel_s_vdw,&
128 iatel_e_vdw,iatscp_s,iatscp_e,ispp,iscp
129 integer :: iatsc_s_nucl,iatsc_e_nucl,iatel_s_nucl,iatel_e_nucl,&
130 iatel_s_vdw_nucl,iatel_e_vdw_nucl,iatscp_s_nucl,iatscp_e_nucl,&
133 ! 12/1/95 Array EPS included in the COMMON block.
135 real(kind=8),dimension(:,:),allocatable :: sigma !(0:ntyp1,0:ntyp1)
136 real(kind=8),dimension(:,:),allocatable :: eps,epslip,sigmaii,&
137 rs0,chi,r0,r0e !(ntyp,ntyp) r0e !!! nie używane
138 real(kind=8),dimension(:),allocatable :: chip,alp,sigma0,&
140 real(kind=8),dimension(2,2) :: rpp,epp,elpp6,elpp3
141 real(kind=8),dimension(:,:),allocatable :: sigma_nucl !(0:ntyp1,0:ntyp1)
142 real(kind=8),dimension(:,:),allocatable :: eps_nucl,sigmaii_nucl,&
143 chi_nucl,r0_nucl, chip_nucl !(ntyp,ntyp) r0e !!! nie używane
144 real(kind=8),dimension(:),allocatable :: alp_nucl,sigma0_nucl,&
145 sigii_nucl,rr0_nucl !(ntyp)
146 real(kind=8),dimension(2,2) :: rpp_nucl,epp_nucl
147 real(kind=8),dimension(:,:),allocatable ::elpp6_nucl,&
148 elpp3_nucl,elpp32_nucl,elpp63_nucl
149 real(kind=8):: r0pp,epspp,AEES,BEES
151 real(kind=8),dimension(:,:),allocatable :: r0d,eps_scp,rscp !(ntyp,2) r0d !!! nie używane
152 real(kind=8),dimension(:),allocatable :: eps_scp_nucl,rscp_nucl!(ntyp,2) r0d !!! nie używane
154 ! 12/5/03 modified 09/18/03 Bond stretching parameters.
156 real(kind=8) :: vbldp0,akp,distchainmax,vbldpDUM
157 real(kind=8),dimension(:,:),allocatable :: vbldsc0,aksc,abond0 !(maxbondterm,ntyp)
158 real(kind=8) :: vbldp0_nucl,akp_nucl
159 real(kind=8),dimension(:,:),allocatable :: vbldsc0_nucl,&
160 aksc_nucl,abond0_nucl !(maxbondterm,ntyp)
162 integer,dimension(:),allocatable :: nbondterm !(ntyp)
163 integer,dimension(:),allocatable :: nbondterm_nucl !(ntyp)
167 integer,dimension(:,:),allocatable :: nterm_scend !(ntyp)
168 real(kind=8),dimension(:,:,:),allocatable:: arotam_end
169 !-----------------------------------------------------------------------------
171 ! Parameters of ab initio-derived potential of virtual-bond-angle bending
172 ! common /theta_abinitio/
173 integer :: nthetyp,ntheterm,ntheterm2,ntheterm3,nsingle,&
175 integer,dimension(:),allocatable :: ithetyp !(-ntyp1:ntyp1)
176 integer,dimension(:,:),allocatable :: nstate !(-ntyp1:ntyp1)
177 real(kind=8),dimension(:,:,:,:),allocatable :: aa0thet
178 !(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
179 real(kind=8),dimension(:,:,:,:,:),allocatable :: aathet
180 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: bbthet,&
182 !(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
183 real(kind=8),dimension(:,:,:,:,:,:,:),allocatable :: ffthet,ggthet
185 !-----------nucleic acid parameters--------------------------
186 integer :: nthetyp_nucl,ntheterm_nucl,ntheterm2_nucl,&
187 ntheterm3_nucl,nsingle_nucl,&
188 ndouble_nucl,nntheterm_nucl
189 integer,dimension(:),allocatable :: ithetyp_nucl !(-ntyp1:ntyp1)
190 real(kind=8),dimension(:,:,:),allocatable :: aa0thet_nucl
191 !(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
192 real(kind=8),dimension(:,:,:,:),allocatable :: aathet_nucl
193 real(kind=8),dimension(:,:,:,:,:),allocatable :: bbthet_nucl,&
194 ccthet_nucl,ddthet_nucl,eethet_nucl
195 !(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
196 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: ffthet_nucl,ggthet_nucl
198 !(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
199 ! Parameters of the virtual-bond-angle probability distribution
201 real(kind=8),dimension(:),allocatable :: a0thet,theta0,&
202 sig0,sigc0 !(-ntyp:ntyp)
203 real(kind=8),dimension(:,:,:,:),allocatable :: athet,bthet !(2,-ntyp:ntyp,-1:1,-1:1)
204 real(kind=8),dimension(:,:),allocatable :: polthet !(0:3,-ntyp:ntyp)
205 real(kind=8),dimension(:,:),allocatable :: gthet !(3,-ntyp:ntyp)
206 ! Parameters of the side-chain probability distribution
208 real(kind=8),dimension(:),allocatable :: dsc,dsc_inv,dsc0 !(ntyp1)
209 real(kind=8),dimension(:,:),allocatable :: bsc !(maxlob,ntyp)
210 real(kind=8),dimension(:,:,:),allocatable :: censc !(3,maxlob,-ntyp:ntyp)
211 real(kind=8),dimension(:,:,:,:),allocatable :: gaussc !(3,3,maxlob,-ntyp:ntyp)
212 integer,dimension(:),allocatable :: nlob !(ntyp1)
213 ! Virtual-bond lenghts
215 real(kind=8) :: vbl,vblinv,vblinv2,vbl_cis,vbl0
217 integer :: loc_start,loc_end,ithet_start,ithet_end,iphi_start,&
218 iphi_end,iphid_start,iphid_end,ibond_start,ibond_end,&
219 ibondp_start,ibondp_end,ivec_start,ivec_end,iset_start,iset_end,&
220 iturn3_start,iturn3_end,iturn4_start,iturn4_end,iint_start,&
221 iint_end,iphi1_start,iphi1_end,itau_start,itau_end,&
222 ilip_start,ilip_end,itube_start,itube_end
223 integer :: ibond_nucl_start,ibond_nucl_end,iphi_nucl_start,&
224 iphi_nucl_end,iphid_nucl_start,iphid_nucl_end,&
225 ibondp_nucl_start,ibondp_nucl_end,ithet_nucl_start,ithet_nucl_end,&
226 loc_start_nucl,loc_end_nucl
227 integer :: icatb_start,icatb_end
228 integer,dimension(:),allocatable :: ibond_displ,ibond_count,&
229 ithet_displ,ithet_count,iphi_displ,iphi_count,iphi1_displ,&
230 iphi1_count,ivec_displ,ivec_count,iset_displ,iset_count,&
231 iint_count,iint_displ !(0:max_fg_procs-1)
232 !-----------------------------------------------------------------------------
235 real(kind=8),dimension(:,:),allocatable :: gcart,gxcart !(3,0:MAXRES)
236 real(kind=8),dimension(:,:),allocatable :: gradcag,gradxag !(3,MAXRES) !!! nie używane
237 ! common /back_constr/
238 integer :: nfrag_back
239 real(kind=8) :: uconst_back
240 real(kind=8),dimension(:),allocatable :: utheta,ugamma,uscdiff !(maxfrag_back)
241 real(kind=8),dimension(:,:,:),allocatable :: wfrag_back !(3,maxfrag_back,maxprocs/20)
242 integer,dimension(:,:,:),allocatable :: ifrag_back !(3,maxfrag_back,maxprocs/20)
243 ! common /qmeas/ in module geometry
244 !-----------------------------------------------------------------------------
247 real(kind=8) :: ss_depth,ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss
248 integer :: ns,nss,nfree
249 integer,dimension(:),allocatable :: iss !(maxss)
251 real(kind=8),dimension(:),allocatable :: dhpb,forcon,dhpb1,fordepth !(maxdim) !el dhpb1 !!! nie używane
253 integer,dimension(:),allocatable :: ihpb,jhpb,ibecarb !(maxdim) !el ibecarb !!! nie używane
254 ! common /restraints/
255 real(kind=8) :: weidis
256 ! common /links_split/
257 integer :: link_start,link_end
258 ! common /dyn_ssbond/
259 real(kind=8) :: Ht,atriss,btriss,ctriss,dtriss
260 integer,dimension(:),allocatable :: idssb,jdssb !(maxdim)
262 logical,dimension(:),allocatable :: dyn_ss_mask !(maxres)
263 !-----------------------------------------------------------------------------
265 ! Parameters of the SCCOR term
267 real(kind=8),dimension(:,:,:,:),allocatable :: v1sccor,v2sccor !(maxterm_sccor,3,-ntyp:ntyp,-ntyp:ntyp)
268 real(kind=8),dimension(:,:,:),allocatable :: v0sccor !(maxterm_sccor,-ntyp:ntyp,-ntyp:ntyp)
270 integer,dimension(:),allocatable :: isccortyp !(-ntyp:ntyp)
271 integer,dimension(:,:),allocatable :: nterm_sccor,nlor_sccor !(-ntyp:ntyp,-ntyp:ntyp)
272 real(kind=8),dimension(:,:,:),allocatable :: vlor1sccor,&
273 vlor2sccor,vlor3sccor !(maxterm_sccor,20,20)
274 real(kind=8),dimension(:,:,:),allocatable :: gloc_sc !(3,0:maxres2,10)
275 real(kind=8),dimension(:,:,:,:),allocatable :: dtauangle !(3,3,3,maxres2)
276 !-----------------------------------------------------------------------------
278 ! Parameters of the SC rotamers (local) term
280 real(kind=8),dimension(:,:),allocatable :: sc_parmin !(maxsccoef,ntyp)
281 real(kind=8),dimension(:,:),allocatable :: sc_parmin_nucl !(maxsccoef,ntyp)
283 !-----------------------------------------------------------------------------
286 integer :: ndih_constr,ndih_nconstr,ntheta_constr
287 integer,dimension(:),allocatable :: idih_constr,idih_nconstr,itheta_constr !(maxdih_constr)
288 integer :: idihconstr_start,idihconstr_end, &
289 ithetaconstr_start,ithetaconstr_end
290 ! real(kind=8) :: ftors
291 real(kind=8),dimension(:),allocatable :: drange,theta_constr0,theta_drange !(maxdih_constr)
292 real(kind=8),dimension(:),allocatable :: phi0,ftors !(maxdih_constr)
293 real(kind=8),dimension(:),allocatable :: for_thet_constr !(maxdih_constr)
295 !-----------------------------------------------------------------------------
297 ! Torsional constants of the rotation about virtual-bond dihedral angles
299 real(kind=8),dimension(:,:,:),allocatable :: v0 !(-maxtor:maxtor,-maxtor:maxtor,2)
301 real(kind=8),dimension(:,:,:),allocatable :: v1,v2 !(maxterm,-maxtor:maxtor,-maxtor:maxtor)
303 real(kind=8),dimension(:,:,:,:),allocatable :: v1,v2 !(maxterm,-maxtor:maxtor,-maxtor:maxtor,2)
305 real(kind=8),dimension(:,:,:),allocatable :: vlor1 !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
306 real(kind=8),dimension(:,:,:),allocatable :: vlor2,vlor3 !(maxlor,maxtor,maxtor)
307 integer,dimension(:),allocatable :: itortyp !(-ntyp1:ntyp1)
308 integer,dimension(:,:,:),allocatable :: nterm,nlor !(-maxtor:maxtor,-maxtor:maxtor,2)
309 ! ---- for rigorous approach
310 integer :: ntortyp,nterm_old
312 integer,dimension(:,:),allocatable :: nterm_kcc_Tb,nterm_kcc
313 integer,dimension(:),allocatable :: iloctyp,itype2loc
314 real(kind=8),dimension(:,:,:,:,:),allocatable :: v1_kcc,v2_kcc
315 real(kind=8),dimension(:,:),allocatable :: v1bend_chyb
316 integer,dimension(:),allocatable :: nbend_kcc_Tb
317 !------torsion nucleic
318 real(kind=8),dimension(:,:),allocatable :: v0_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
319 real(kind=8),dimension(:,:,:),allocatable :: v1_nucl,v2_nucl !(maxterm,-maxtor:maxtor,-maxtor:maxtor)
320 real(kind=8),dimension(:,:,:),allocatable :: vlor1_nucl !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
321 real(kind=8),dimension(:,:,:),allocatable :: vlor2_nucl,vlor3_nucl !(maxlor,maxtor,maxtor)
322 integer,dimension(:),allocatable :: itortyp_nucl !(-ntyp1:ntyp1)
323 integer,dimension(:,:),allocatable :: nterm_nucl,nlor_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
324 integer :: ntortyp_nucl,nterm_old_nucl
326 ! 6/23/01 - constants for double torsionals
328 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: v1c,v1s
329 !(2,maxtermd_1,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
330 real(kind=8),dimension(:,:,:,:,:,:),allocatable :: v2c,v2s
331 !(maxtermd_2,maxtermd_2,-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
332 integer,dimension(:,:,:,:),allocatable :: ntermd_1,ntermd_2
333 !(-maxtor:maxtor,-maxtor:maxtor,-maxtor:maxtor,2)
334 ! 9/18/99 - added Fourier coeffficients of the expansion of local energy
337 real(kind=8),dimension(:,:),allocatable :: b1,b2,&
338 b1tilde,b2tilde,gtb1,gtb2!(2,-maxtor:maxtor),
339 real(kind=8),dimension(:,:,:),allocatable :: cc,dd,ee,&
340 ctilde,dtilde,bnew1,bnew2,ccnew,ddnew,bnew1tor,&
341 bnew2tor,ccnewtor,ddnewtor,ccold,ddold,eeold,&
343 real(kind=8),dimension(:,:,:,:),allocatable :: eenew,eenewtor
344 real(kind=8),dimension(:,:),allocatable :: e0new,e0newtor
346 ! common/fourier/ z wham
347 real(kind=8),dimension(:,:),allocatable :: b !(13,0:maxtor)
348 !---------------MOMO---------------------------------------------------
349 integer,dimension(:),allocatable :: icharge
350 real(kind=8),dimension(:,:),allocatable :: alphapol,epshead,&
351 sig0head,sigiso1,sigiso2,rborn,sigmap1,sigmap2,chis,wquad,chipp,&
353 real(kind=8),dimension(:,:,:),allocatable :: alphasur,alphiso,&
355 real(kind=8),dimension(:,:,:,:),allocatable :: dhead
356 !-----------------------------------------------------------------------------
358 ! Varibles for cutoff on electorstatic
359 real(kind=8) sss_ele_cut,sss_ele_grad
360 integer xshift,yshift,zshift
361 !2 Jul 2017 lipidc parameters -----------------------------------------------------
362 real(kind=8),dimension(:), allocatable :: liptranene
363 real(kind=8) :: pepliptran
365 ! 4 Jul 2017 parameters for shieliding
366 real(kind=8),dimension(:), allocatable :: long_r_sidechain, &
368 real(kind=8) :: VSolvSphere,VSolvSphere_div,buff_shield
370 real(kind=8) :: distafminit,forceAFMconst,velAFMconst,&
371 velnanoconst,distnanoinit,forcenanoconst,inanomove,vecsim,vectrue
372 real(kind=8),dimension(1000) :: inanotab
373 integer :: afmend,afmbeg,nbegafmmat,nendafmmat
374 integer, dimension(1000) :: afmendcentr,afmbegcentr
375 real(kind=8),dimension(:,:), allocatable :: catprm
376 real(kind=8),dimension(:,:,:), allocatable :: catnuclprm
379 real(kind=8),dimension(:,:), allocatable :: eps_scbase, &
381 sigmap1_scbase,sigmap2_scbase, &
382 dhead_scbasei, dhead_scbasej, epshead_scbase,&
383 sig0head_scbase, rborn_scbasei,rborn_scbasej,alphapol_scbase,epsintab_scbase,&
385 real(kind=8),dimension(:,:,:), allocatable :: alphasur_scbase, &
386 wdipdip_scbase,wqdip_scbase,chi_scbase,chipp_scbase,chis_scbase
388 real(kind=8),dimension(:), allocatable :: eps_pepbase, &
390 sigmap1_pepbase,sigmap2_pepbase,&
391 aa_pepbase,bb_pepbase
393 real(kind=8),dimension(:,:), allocatable :: alphasur_pepbase, &
394 wdipdip_pepbase,chi_pepbase,chipp_pepbase,chis_pepbase
396 real(kind=8),dimension(:), allocatable :: eps_scpho, &
398 sigmap1_scpho,sigmap2_scpho,&
399 aa_scpho,bb_scpho,wqq_scpho,epsintab_scpho,alphapol_scpho,&
400 rborn_scphoi,rborn_scphoj,dhead_scphoi,alphi_scpho
402 real(kind=8),dimension(:,:), allocatable :: alphasur_scpho, &
403 chi_scpho,chipp_scpho,chis_scpho, &
405 real(kind=8) ,dimension(4) :: alphasur_peppho
406 real(kind=8) ,dimension(2) :: wqdip_peppho
407 real(kind=8) :: eps_peppho,sigma_peppho,sigmap1_peppho,sigmap2_peppho, &
409 !------------- for psi prec constraints
410 real(kind=8),dimension(:,:), allocatable :: vpsipred,sdihed
412 !23 Jul 2019 ions parameters by Agnieszka Lipska (Ca, K, Na, Mg, Cl)--------------------
413 ! real(kind=8),dimension(:,:),allocatable :: alphapolcat,&
414 ! epsheadcat,sig0headcat,sigiso1cat,sigiso2cat,sigmap1cat,&
415 ! sigmap2cat,wquadcat,chicat,chiscat,chippcat,&
416 ! epsintabcat,debaykapcat
417 integer,dimension(:),allocatable :: ichargecat
420 real(kind=8),dimension(:,:),allocatable :: alphapolcat, alphapolcat2, &
421 epsheadcat,sig0headcat,sigiso1cat,sigiso2cat,rborn1cat,rborn2cat,&
422 sigmap1cat,sigmap2cat,chis1cat,chis2cat,wquadcat,chipp1cat,chipp2cat,&
423 epsintabcat,debaykapcat,chi1cat,chi2cat,sigmacat, nstatecat, epscat,&
426 real(kind=8),dimension(:,:,:),allocatable :: alphasurcat,&
427 alphisocat,wqdipcat,dtailcat,wstatecat
428 real(kind=8),dimension(:,:,:,:),allocatable :: dheadcat
431 real(kind=8),dimension(:,:),allocatable :: alphapolmart, alphapolmart2, &
432 epsheadmart,sig0headmart,sigiso1mart,sigiso2mart,rborn1mart,rborn2mart,&
433 sigmap1mart,sigmap2mart,chis1mart,chis2mart,wquadmart,chipp1mart,chipp2mart,&
434 epsintabmart,debaykapmart,chi1mart,chi2mart,sigmamart, nstatemart, epsmart,&
435 aa_aq_mart,bb_aq_mart
437 real(kind=8),dimension(:,:,:),allocatable :: alphasurmart,&
438 alphisomart,wqdipmart,dtailmart,wstatemart
439 real(kind=8),dimension(:,:,:,:),allocatable :: dheadmart
442 integer,dimension(60000) :: contlistscpi_f,contlistscpj_f
443 ! integer :: ifirstrun,ilist_scp_first
444 ! real(kind=8),dimension(:,:),allocatable :: alphapol,epshead,&
445 ! sig0head,sigiso1,sigiso2,rborn,sigmap1,sigmap2,chis,wquad,chipp,&
449 !end of ions parameters by Agnieszka Lipska (Ca, K, Na, Mg, Cl)-----------------------
452 ! Parameters for transistion ions
453 real(kind=8),dimension(:,:,:),allocatable:: agamacattran,&
455 real(kind=8),dimension(:,:),allocatable::acatshiftdsc,&
456 bcatshiftdsc,demorsecat,alphamorsecat,x0catleft,x0catright,&
458 real(kind=8),dimension(:),allocatable::ntrantyp
460 ! FRAGMENT FOR INTERACTION LIST
461 integer,dimension(:),allocatable :: newcontlistppi,newcontlistppj,&
462 newcontlisti,newcontlistj, newcontlistscpi,newcontlistscpj,&
463 newcontlistcatscnormi,newcontlistcatscnormj,&
464 newcontlistcatpnormi,newcontlistcatpnormj,&
465 newcontlistcatsctrani,newcontlistcatsctranj,&
466 newcontlistcatptrani,newcontlistcatptranj,&
467 newcontlistcatscangi,newcontlistcatscangj,&
468 newcontlistcatscangfi,newcontlistcatscangfj,&
469 newcontlistcatscangfk,&
470 newcontlistcatscangti,newcontlistcatscangtj,&
471 newcontlistcatscangtk,newcontlistcatscangtl,&
472 newcontlistcatcatnormi,newcontlistcatcatnormj,&
473 newcontlistmartsci,newcontlistmartscj,&
474 newcontlistmartpi,newcontlistmartpj
480 integer :: g_listpp_start,g_listpp_end,g_listscp_start,g_listscp_end,&
481 g_listscsc_start,g_listscsc_end, &
482 g_listcatsctran_start,g_listcatsctran_end,&
483 g_listcatscnorm_start,g_listcatscnorm_end,&
484 g_listcatptran_start,g_listcatptran_end,&
485 g_listcatpnorm_start,g_listcatpnorm_end,&
486 g_ilist_catscnorm,g_ilist_catsctran,g_ilist_catpnorm,&
487 g_ilist_catptran,g_ilist_catscang,g_ilist_catscangf,g_ilist_catscangt,&
488 g_listcatscang_start,g_listcatscang_end,&
489 g_listcatscangf_start,g_listcatscangf_end,&
490 g_listcatscangt_start,g_listcatscangt_end,&
491 g_listcatcatnorm_start,g_listcatcatnorm_end,g_ilist_catcatnorm,&
492 g_ilist_martp,g_ilist_martsc,&
493 g_listmartsc_start,g_listmartsc_end,&
494 g_listmartp_start,g_listmartp_end
498 ! MARTINI FORCE FIELD
499 integer :: ilipbond_start,ilipbond_end,ilipang_start,ilipang_end, &
500 maxelecliplist,ilip_elec_start,ilipelec_end,maxljliplist,iliplj_start,iliplj_end,&
501 ilipbond_start_tub,ilipbond_end_tub
502 integer,dimension(:),allocatable :: mlipljlisti,mlipljlistj,&
503 mlipeleclisti,mlipeleclistj
504 real(kind=8),dimension(:,:,:),allocatable :: lip_angle_force,lip_angle_angle
505 real(kind=8),dimension(:,:),allocatable :: lip_bond,lip_eps,lip_sig
506 integer,dimension(:),allocatable :: ichargelipid
507 real(kind=8) :: kjtokcal,krad,k_coulomb_lip,kbondlip
509 integer :: inprint,npermut,&
510 tubelog,constr_homology,homol_nset
511 logical :: mremd_dec,out_cart,&
513 with_dihed_constr,read2sigma,start_from_model,read_homol_frag,&
514 out_template_coord,out_template_restr,loc_qlike,adaptive
515 real(kind=8) :: aincr,waga_dist,waga_angle,waga_theta,&
517 real(kind=8),dimension(:),allocatable :: waga_homology
518 real(kind=8),dimension(:,:),allocatable :: odl,&
519 sigma_odl,dih,sigma_dih, sigma_odlir, xxtpl,&
520 yytpl,zztpl,thetatpl,sigma_theta,sigma_d
521 integer,dimension(:),allocatable :: ires_homo,jres_homo
522 integer,dimension(:,:),allocatable :: idomain,tabpermchain,iequiv,&
523 chain_border,chain_border1
524 integer :: lim_odl,lim_dih,link_start_homo,&
525 link_end_homo,idihconstr_start_homo,idihconstr_end_homo
526 logical,dimension(:,:),allocatable :: l_homo
527 integer ::nchain,iprzes,&
530 nmodel_start,nran_start
531 ! real(kind=8),dimension(:,:),allocatable :: c,dc,dc_old,xloc,xrot,&
532 ! dc_norm,dc_norm2,cref,crefjlee
533 ! real(kind=8),dimension(:),allocatable :: d_c_work
534 real(kind=8),dimension(:,:,:),allocatable :: chomo
535 ! real(kind=8) :: totTafm
536 character(len=256),dimension(:),allocatable:: pdbfiles_chomo
537 integer,dimension(:),allocatable :: chain_length,ireschain,&
538 nequiv,mapchain, nres_chomo
539 real(kind=8) :: enecut,sscut,sss,sssgrad
541 real(kind=8),dimension(:),allocatable :: awaterenta,bwaterenta,&
542 cwaterenta,dwaterenta,awaterentro,bwaterentro,cwaterentro,&
544 ! buflipbot, bufliptop,bordlipbot,bordliptop,lipbufthick,lipthick
545 !-------------------------------------------------------------------------
546 real(kind=8),dimension(3,70000) :: ea
549 integer niter,nfun,ncalls
551 ! real(kind=8) :: buftubebot, buftubetop,bordtubebot,bordtubetop,tubebufthick
552 end module energy_data