X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?a=blobdiff_plain;f=source%2Funres%2Fdata%2Fenergy_data.f90;h=844aa85eb0450948daf413fdc65115a8689c05af;hb=e1aeda758c35ccdf5a5b88e825b6ca391c2dc1ae;hp=11382e28e05f02562918360ef74ecb24724c5cfa;hpb=299e2c41124d3fa8adba7244716515a2cc160ed1;p=unres4.git

diff --git a/source/unres/data/energy_data.f90 b/source/unres/data/energy_data.f90
index 11382e2..844aa85 100644
--- a/source/unres/data/energy_data.f90
+++ b/source/unres/data/energy_data.f90
@@ -64,7 +64,9 @@
       integer :: rescale_mode
       real(kind=8) :: wsc,wscp,welec,wbond,wstrain,wtor,wtor_d,wang,&
        wscloc,wcorr,wcorr4,wcorr5,wcorr6,wsccor,wel_loc,wturn3,wturn4,&
-       wturn6,wvdwpp
+       wturn6,wvdwpp,wliptran,wshield,lipscale,wtube, &
+       wbond_nucl,wang_nucl,wcorr_nucl,wcorr3_nucl,welpp,wtor_nucl,&
+       wtor_d_nucl,welsb,wsbloc,wvdwsb,welpsb,wvdwpsb
 #ifdef CLUSTER
       real(kind=8) :: scalscp
 #endif
@@ -88,20 +90,27 @@
 !-----------------------------------------------------------------------------
 ! common.interact
 !      common /interact/
-      real(kind=8),dimension(:,:),allocatable :: aa,bb,augm !(ntyp,ntyp)
+      real(kind=8),dimension(:,:),allocatable :: aa_aq,bb_aq,augm,aa_lip,bb_lip !(ntyp,ntyp)
+      real(kind=8),dimension(:),allocatable :: sc_aa_tube_par,sc_bb_tube_par,&
+       acavtub,bcavtub,ccavtub,dcavtub,tubetranene
+      real(kind=8) :: acavtubpep,bcavtubpep,ccavtubpep,dcavtubpep, &
+      tubetranenepep,pep_aa_tube,pep_bb_tube,tubeR0
+      real(kind=8),dimension(3) :: tubecenter
       real(kind=8),dimension(:,:),allocatable :: aad,bad !(ntyp,2)
       real(kind=8),dimension(2,2) :: app,bpp,ael6,ael3
       integer :: expon,expon2, nnt,nct,itypro
       integer,dimension(:,:),allocatable :: istart,iend !(maxres,maxint_gr)
-      integer,dimension(:),allocatable :: nint_gr,itype,itel,&
+      integer,dimension(:),allocatable :: nint_gr,itel,&
        ielstart,ielend,ielstart_vdw,ielend_vdw,nscp_gr !(maxres)
+      integer,dimension(:),allocatable :: istype,molnum
+      integer,dimension(:,:),allocatable :: itype ! now itype has more molecule types
       integer,dimension(:,:),allocatable :: iscpstart,iscpend !(maxres,maxint_gr)
       integer :: iatsc_s,iatsc_e,iatel_s,iatel_e,iatel_s_vdw,&
        iatel_e_vdw,iatscp_s,iatscp_e,ispp,iscp
 ! 12/1/95 Array EPS included in the COMMON block.
 !      common /body/
       real(kind=8),dimension(:,:),allocatable :: sigma !(0:ntyp1,0:ntyp1)
-      real(kind=8),dimension(:,:),allocatable :: eps,sigmaii,&
+      real(kind=8),dimension(:,:),allocatable :: eps,epslip,sigmaii,&
        rs0,chi,r0,r0e	!(ntyp,ntyp) r0e !!! nie używane
       real(kind=8),dimension(:),allocatable :: chip,alp,sigma0,&
        sigii,rr0	!(ntyp)
@@ -109,9 +118,15 @@
       real(kind=8),dimension(:,:),allocatable :: r0d,eps_scp,rscp !(ntyp,2)  r0d  !!! nie używane
 ! 12/5/03 modified 09/18/03 Bond stretching parameters.
 !      common /stretch/
-      real(kind=8) :: vbldp0,akp,distchainmax
+      real(kind=8) :: vbldp0,akp,distchainmax,vbldpDUM
       real(kind=8),dimension(:,:),allocatable :: vbldsc0,aksc,abond0 !(maxbondterm,ntyp)
+      real(kind=8) :: vbldp0_nucl,akp_nucl
+      real(kind=8),dimension(:,:),allocatable :: vbldsc0_nucl,&
+       aksc_nucl,abond0_nucl !(maxbondterm,ntyp)
+
       integer,dimension(:),allocatable :: nbondterm	!(ntyp)
+      integer,dimension(:),allocatable :: nbondterm_nucl     !(ntyp)
+
 !-----------------------------------------------------------------------------
 ! common.local
 ! Parameters of ab initio-derived potential of virtual-bond-angle bending
@@ -126,6 +141,20 @@
        ccthet,ddthet,eethet
 !(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
       real(kind=8),dimension(:,:,:,:,:,:,:),allocatable :: ffthet,ggthet
+
+!-----------nucleic acid parameters--------------------------
+      integer :: nthetyp_nucl,ntheterm_nucl,ntheterm2_nucl,&
+      ntheterm3_nucl,nsingle_nucl,&
+       ndouble_nucl,nntheterm_nucl
+      integer,dimension(:),allocatable :: ithetyp_nucl !(-ntyp1:ntyp1)
+      real(kind=8),dimension(:,:,:),allocatable :: aa0thet_nucl
+!(-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+      real(kind=8),dimension(:,:,:,:),allocatable :: aathet_nucl
+      real(kind=8),dimension(:,:,:,:,:),allocatable :: bbthet_nucl,&
+       ccthet_nucl,ddthet_nucl,eethet_nucl
+!(maxsingle,maxtheterm2,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
+      real(kind=8),dimension(:,:,:,:,:,:),allocatable :: ffthet_nucl,ggthet_nucl
+
 !(maxdouble,maxdouble,maxtheterm3,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,-maxthetyp1:maxthetyp1,2)
 ! Parameters of the virtual-bond-angle probability distribution
 !      common /thetas/ 
@@ -149,7 +178,11 @@
        iphi_end,iphid_start,iphid_end,ibond_start,ibond_end,&
        ibondp_start,ibondp_end,ivec_start,ivec_end,iset_start,iset_end,&
        iturn3_start,iturn3_end,iturn4_start,iturn4_end,iint_start,&
-       iint_end,iphi1_start,iphi1_end,itau_start,itau_end
+       iint_end,iphi1_start,iphi1_end,itau_start,itau_end,&
+       ilip_start,ilip_end,itube_start,itube_end
+      integer :: ibond_nucl_start,ibond_nucl_end,iphi_nucl_start,&
+       iphi_nucl_end,iphid_nucl_start,iphid_nucl_end,& 
+       ibondp_nucl_start,ibondp_nucl_end,ithet_nucl_start,ithet_nucl_end
       integer,dimension(:),allocatable :: ibond_displ,ibond_count,&
        ithet_displ,ithet_count,iphi_displ,iphi_count,iphi1_displ,&
        iphi1_count,ivec_displ,ivec_count,iset_displ,iset_count,&
@@ -165,18 +198,7 @@
       real(kind=8),dimension(:),allocatable :: utheta,ugamma,uscdiff !(maxfrag_back)
       real(kind=8),dimension(:,:,:),allocatable :: wfrag_back !(3,maxfrag_back,maxprocs/20)
       integer,dimension(:,:,:),allocatable :: ifrag_back !(3,maxfrag_back,maxprocs/20)
-!      common /qmeas/
-      real(kind=8),dimension(50) :: qfrag
-      real(kind=8),dimension(100) :: qpair
-      real(kind=8),dimension(:,:),allocatable :: qinfrag,wfrag !(50,maxprocs/20)
-      real(kind=8),dimension(:,:),allocatable :: qinpair,wpair !(100,maxprocs/20)
-      real(kind=8) :: eq_time,Uconst
-      integer :: iset,nset
-      integer,dimension(:),allocatable :: mset !(maxprocs/20)
-      integer,dimension(:,:,:),allocatable :: ifrag !(2,50,maxprocs/20)
-      integer,dimension(:,:,:),allocatable :: ipair !(2,100,maxprocs/20)
-      integer :: nfrag,npair
-      logical :: usampl
+!      common /qmeas/ in module geometry
 !-----------------------------------------------------------------------------
 ! common.sbridge
 !      common /sbridge/
@@ -184,7 +206,7 @@
       integer :: ns,nss,nfree
       integer,dimension(:),allocatable :: iss	!(maxss)
 !      common /links/
-      real(kind=8),dimension(:),allocatable :: dhpb,forcon,dhpb1 !(maxdim) !el dhpb1 !!! nie używane
+      real(kind=8),dimension(:),allocatable :: dhpb,forcon,dhpb1,fordepth !(maxdim) !el dhpb1 !!! nie używane
       integer :: nhpb
       integer,dimension(:),allocatable :: ihpb,jhpb,ibecarb !(maxdim) !el ibecarb !!! nie używane
 !      common /restraints/
@@ -192,7 +214,7 @@
 !      common /links_split/
       integer :: link_start,link_end
 !      common /dyn_ssbond/
-      real(kind=8) :: Ht
+      real(kind=8) :: Ht,atriss,btriss,ctriss,dtriss
       integer,dimension(:),allocatable :: idssb,jdssb !(maxdim)
       logical :: dyn_ss
       logical,dimension(:),allocatable :: dyn_ss_mask !(maxres)
@@ -217,12 +239,15 @@
 !-----------------------------------------------------------------------------
 ! common.torcnstr
 !      common /torcnstr/
-      integer :: ndih_constr,ndih_nconstr
-      integer,dimension(:),allocatable :: idih_constr,idih_nconstr !(maxdih_constr)
-      integer :: idihconstr_start,idihconstr_end
+      integer :: ndih_constr,ndih_nconstr,ntheta_constr
+      integer,dimension(:),allocatable :: idih_constr,idih_nconstr,itheta_constr !(maxdih_constr)
+      integer :: idihconstr_start,idihconstr_end, &
+       ithetaconstr_start,ithetaconstr_end
       real(kind=8) :: ftors
-      real(kind=8),dimension(:),allocatable :: drange !(maxdih_constr)
+      real(kind=8),dimension(:),allocatable :: drange,theta_constr0,theta_drange !(maxdih_constr)
       real(kind=8),dimension(:),allocatable :: phi0 !(maxdih_constr)
+      real(kind=8),dimension(:),allocatable :: for_thet_constr !(maxdih_constr)
+
 !-----------------------------------------------------------------------------
 ! common.torsion
 ! Torsional constants of the rotation about virtual-bond dihedral angles
@@ -238,6 +263,15 @@
       integer,dimension(:),allocatable :: itortyp !(-ntyp1:ntyp1)
       integer,dimension(:,:,:),allocatable :: nterm,nlor !(-maxtor:maxtor,-maxtor:maxtor,2)
       integer :: ntortyp,nterm_old
+!------torsion nucleic
+      real(kind=8),dimension(:,:),allocatable :: v0_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
+      real(kind=8),dimension(:,:,:),allocatable :: v1_nucl,v2_nucl !(maxterm,-maxtor:maxtor,-maxtor:maxtor)
+      real(kind=8),dimension(:,:,:),allocatable :: vlor1_nucl !(maxlor,-maxtor:maxtor,-maxtor:maxtor)
+      real(kind=8),dimension(:,:,:),allocatable :: vlor2_nucl,vlor3_nucl !(maxlor,maxtor,maxtor)
+      integer,dimension(:),allocatable :: itortyp_nucl !(-ntyp1:ntyp1)
+      integer,dimension(:,:),allocatable :: nterm_nucl,nlor_nucl !(-maxtor:maxtor,-maxtor:maxtor,2)
+      integer :: ntortyp_nucl,nterm_old_nucl
+
 ! 6/23/01 - constants for double torsionals
 !      common /torsiond/ 
       real(kind=8),dimension(:,:,:,:,:,:),allocatable :: v1c,v1s 
@@ -257,22 +291,23 @@
 !      common/fourier/  z wham
       real(kind=8),dimension(:,:),allocatable :: b !(13,0:maxtor)
 !-----------------------------------------------------------------------------
-! common.var
-! Store the geometric variables in the following COMMON block.
-!      common /var/ in module geometry_data
-! Store the angles and variables corresponding to old conformations (for use
-! in MCM).
-!      common /oldgeo/
-!el      real(kind=8),dimension(:,:),allocatable :: varsave !(maxvar,maxsave)
-!      real(kind=8),dimension(:),allocatable :: esave !(maxsave)
-!      integer,dimension(:),allocatable :: Origin !(maxsave)
-!      integer :: nstore
-! freeze some variables
-!      common /restr/
-      real(kind=8),dimension(:),allocatable :: varall !(maxvar)
-      integer,dimension(:),allocatable :: mask_theta,&
-       mask_phi,mask_side !(maxres)
-      logical :: mask_r
-!-----------------------------------------------------------------------------
-!-----------------------------------------------------------------------------
+! 24 Apr 2017 
+! Varibles for cutoff on electorstatic
+      real(kind=8) sss_ele_cut,sss_ele_grad
+      integer xshift,yshift,zshift
+!2 Jul 2017 lipidc parameters -----------------------------------------------------
+      real(kind=8),dimension(:), allocatable :: liptranene
+      real(kind=8) :: pepliptran
+
+! 4 Jul 2017 parameters for shieliding 
+      real(kind=8),dimension(:), allocatable :: long_r_sidechain, &
+        short_r_sidechain
+      real(kind=8) :: VSolvSphere,VSolvSphere_div,buff_shield
+! AFM
+       real(kind=8) :: distafminit,forceAFMconst,velAFMconst
+      integer :: afmend,afmbeg
+
+
+
+
       end module energy_data