WeFold Lorentzian like potentials introduction

diff --git a/source/unres/src_MD-M/COMMON.SBRIDGE b/source/unres/src_MD-M/COMMON.SBRIDGE
index 1d69501..3279b28 100644 (file)
--- a/source/unres/src_MD-M/COMMON.SBRIDGE
+++ b/source/unres/src_MD-M/COMMON.SBRIDGE
@@ -2,9 +2,10 @@
       integer ns,nss,nfree,iss
       common /sbridge/ ss_depth,ebr,d0cm,akcm,akth,akct,v1ss,v2ss,v3ss,
      & ns,nss,nfree,iss(maxss)
-      double precision dhpb,dhpb1,forcon
+      double precision dhpb,dhpb1,forcon,fordepth
       integer ihpb,jhpb,nhpb,idssb,jdssb
       common /links/ dhpb(maxdim),dhpb1(maxdim),forcon(maxdim),
+     & fordepth(maxdim), 
      & ihpb(maxdim),jhpb(maxdim),ibecarb(maxdim),nhpb
       double precision weidis
       common /restraints/ weidis

diff --git a/source/unres/src_MD-M/energy_p_new_barrier.F b/source/unres/src_MD-M/energy_p_new_barrier.F
index 700fb07..cf9ddcb 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -4084,6 +4084,7 @@ C
       include 'COMMON.VAR'
       include 'COMMON.INTERACT'
       include 'COMMON.IOUNITS'
+      include 'COMMON.CONTROL'
       dimension ggg(3)
       ehpb=0.0D0
 cd      write(iout,*)'edis: nhpb=',nhpb,' fbr=',fbr
@@ -4116,21 +4117,72 @@ C 15/02/13 CC dynamic SSbond - additional check
           ehpb=ehpb+2*eij
          endif
 cd          write (iout,*) "eij",eij
+cd   &   ' waga=',waga,' fac=',fac
+        else if (ii.gt.nres .and. jj.gt.nres) then
+c Restraints from contact prediction
+          dd=dist(ii,jj)
+          if (constr_dist.eq.11) then
+            ehpb=ehpb+fordepth(i)**4
+     &          *rlornmr1(dd,dhpb(i),dhpb1(i),forcon(i))
+            fac=fordepth(i)**4
+     &          *rlornmr1prim(dd,dhpb(i),dhpb1(i),forcon(i))/dd
+           else
+          if (dhpb1(i).gt.0.0d0) then
+            ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+            fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c            write (iout,*) "beta nmr",
+c     &        dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+          else
+            dd=dist(ii,jj)
+            rdis=dd-dhpb(i)
+C Get the force constant corresponding to this distance.
+            waga=forcon(i)
+C Calculate the contribution to energy.
+            ehpb=ehpb+waga*rdis*rdis
+c            write (iout,*) "beta reg",dd,waga*rdis*rdis
+C
+C Evaluate gradient.
+C
+            fac=waga*rdis/dd
+          endif
+          endif
+          do j=1,3
+            ggg(j)=fac*(c(j,jj)-c(j,ii))
+          enddo
+          do j=1,3
+            ghpbx(j,iii)=ghpbx(j,iii)-ggg(j)
+            ghpbx(j,jjj)=ghpbx(j,jjj)+ggg(j)
+          enddo
+          do k=1,3
+            ghpbc(k,jjj)=ghpbc(k,jjj)+ggg(k)
+            ghpbc(k,iii)=ghpbc(k,iii)-ggg(k)
+          enddo
         else
 C Calculate the distance between the two points and its difference from the
 C target distance.
           dd=dist(ii,jj)
+          if (constr_dist.eq.11) then
+            ehpb=ehpb+fordepth(i)**4*rlornmr1(dd,dhpb(i),dhpb1(i))
+            fac=fordepth(i)**4*rlornmr1prim(dd,dhpb(i),dhpb1(i))/dd
+           else   
+          if (dhpb1(i).gt.0.0d0) then
+            ehpb=ehpb+2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+            fac=forcon(i)*gnmr1prim(dd,dhpb(i),dhpb1(i))/dd
+c            write (iout,*) "alph nmr",
+c     &        dd,2*forcon(i)*gnmr1(dd,dhpb(i),dhpb1(i))
+          else
             rdis=dd-dhpb(i)
 C Get the force constant corresponding to this distance.
             waga=forcon(i)
 C Calculate the contribution to energy.
             ehpb=ehpb+waga*rdis*rdis
+c            write (iout,*) "alpha reg",dd,waga*rdis*rdis
 C
 C Evaluate gradient.
 C
             fac=waga*rdis/dd
-cd      print *,'i=',i,' ii=',ii,' jj=',jj,' dhpb=',dhpb(i),' dd=',dd,
-cd   &   ' waga=',waga,' fac=',fac
+          endif
+          endif
             do j=1,3
               ggg(j)=fac*(c(j,jj)-c(j,ii))
             enddo
@@ -4154,7 +4206,7 @@ cgrad        enddo
           enddo
         endif
       enddo
-      ehpb=0.5D0*ehpb
+      if (constr_dist.ne.11) ehpb=0.5D0*ehpb
       return
       end
 C--------------------------------------------------------------------------

diff --git a/source/unres/src_MD-M/gnmr1.f b/source/unres/src_MD-M/gnmr1.f
index 905e746..f44e404 100644 (file)
--- a/source/unres/src_MD-M/gnmr1.f
+++ b/source/unres/src_MD-M/gnmr1.f
@@ -41,3 +41,33 @@ c-------------------------------------------------------------------------------
       return
       end
 c---------------------------------------------------------------------------------
+      double precision function rlornmr1(y,ymin,ymax,sigma)
+      implicit none
+      double precision y,ymin,ymax,sigma
+      double precision wykl /4.0d0/
+      if (y.lt.ymin) then
+        rlornmr1=(ymin-y)**wykl/((ymin-y)**wykl+sigma**wykl)
+      else if (y.gt.ymax) then
+        rlornmr1=(y-ymax)**wykl/((y-ymax)**wykl+sigma**wykl)
+      else
+        rlornmr1=0.0d0
+      endif
+      return
+      end
+c------------------------------------------------------------------------------
+      double precision function rlornmr1prim(y,ymin,ymax,sigma)
+      implicit none
+      double precision y,ymin,ymax,sigma
+      double precision wykl /4.0d0/
+      if (y.lt.ymin) then
+        rlornmr1prim=-(ymin-y)**(wykl-1)*sigma**wykl*wykl/
+     &   ((ymin-y)**wykl+sigma**wykl)
+      else if (y.gt.ymax) then
+        rlornmr1prim=(y-ymax)**(wykl-1)*sigma**wykl*wykl/
+     & ((y-ymax)**wykl+sigma**wykl)
+      else
+        rlornmr1prim=0.0d0
+      endif
+      return
+      end
+

diff --git a/source/unres/src_MD-M/readrtns_CSA.F b/source/unres/src_MD-M/readrtns_CSA.F
index 3987a4d..f53da12 100644 (file)
--- a/source/unres/src_MD-M/readrtns_CSA.F
+++ b/source/unres/src_MD-M/readrtns_CSA.F
@@ -2352,10 +2352,27 @@ c            write (iout,*) "j",j," k",k
         endif
       enddo 
       do i=1,ndist_
-        read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
+        if (constr_dist.eq.11) then
+        read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+     &     ibecarb(i),forcon(nhpb+1),fordepth(nhpb+1)
+        fordepth(nhpb+1)=fordepth(nhpb+1)/forcon(nhpb+1)
+        else
+        read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),dhpb(i),dhpb1(i),
+     &     ibecarb(i),forcon(nhpb+1)
+        endif
         if (forcon(nhpb+1).gt.0.0d0) then
           nhpb=nhpb+1
-          dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+          if (ibecarb(i).gt.0) then
+            ihpb(i)=ihpb(i)+nres
+            jhpb(i)=jhpb(i)+nres
+          endif
+          if (dhpb(nhpb).eq.0.0d0)
+     &       dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
+        endif
+C        read (inp,*) ihpb(nhpb+1),jhpb(nhpb+1),forcon(nhpb+1)
+C        if (forcon(nhpb+1).gt.0.0d0) then
+C          nhpb=nhpb+1
+C          dhpb(nhpb)=dist(ihpb(nhpb),jhpb(nhpb))
 #ifdef MPI
           if (.not.out1file .or. me.eq.king)
      &    write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
@@ -2364,7 +2381,7 @@ c            write (iout,*) "j",j," k",k
           write (iout,'(a,3i5,f8.2,f10.1)') "+dist.constr ",
      &     nhpb,ihpb(nhpb),jhpb(nhpb),dhpb(nhpb),forcon(nhpb)
 #endif
-        endif
+
       enddo
       call flush(iout)
       return