small changes

diff --git a/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip b/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip
index 9708c27..2abb67a 100644 (file)
--- a/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip
+++ b/PARAM/sc_GB_opt_ext.1gab_3S_qclass5no310-shan2-sc-16-10-8k_lip
@@ -228,7 +228,7 @@
   -0.1779        −3.4493         3.360749       4.211903
    5.240276       3.016734       3.016734
 
-  -6.5557         2.905459       3.641304       4.530360
+  -9.4378         2.905459       3.641304       4.530360
    2.608049       2.608049
 
    2.252800       2.823350       3.512697       2.022197

diff --git a/PARAM/sc_GB_opt_ext_lip.7p_wham_last b/PARAM/sc_GB_opt_ext_lip.7p_wham_last
index f006f35..4f1f32f 100644 (file)
--- a/PARAM/sc_GB_opt_ext_lip.7p_wham_last
+++ b/PARAM/sc_GB_opt_ext_lip.7p_wham_last
@@ -229,7 +229,7 @@
   -0.1779        -3.4493         3.360749       4.211903
    5.240276       3.016734       3.016734
 
-  -6.5557         2.905459       3.641304       4.530360
+  -9.4378         2.905459       3.641304       4.530360
    2.608049       2.608049
 
    2.252800       2.823350       3.512697       2.022197

diff --git a/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four b/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four
index f99e603..59180ac 100644 (file)
--- a/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four
+++ b/PARAM/sc_GB_opt_ext_lip.7p_wham_last_four
@@ -229,7 +229,7 @@
   -0.1779        -3.4493         3.360749       4.211903
    5.240276       3.016734       3.016734
 
-  -6.5557         2.905459       3.641304       4.530360
+  -9.4378         2.905459       3.641304       4.530360
    2.608049       2.608049
 
    2.252800       2.823350       3.512697       2.022197

diff --git a/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm b/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm
index a4e97f6..c97df64 100644 (file)
--- a/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm
+++ b/PARAM/sc_GB_opt_iter0_7prot-eps_ext_lip.parm
@@ -232,7 +232,7 @@
   -0.1779        -3.4493         3.360749       4.211903
    5.240276       3.016734       3.016734
 
-  -6.5557         2.905459       3.641304       4.530360
+  -9.4379         2.905459       3.641304       4.530360
    2.608049       2.608049
 
    2.252800       2.823350       3.512697       2.022197

diff --git a/PARAM/scinter_GB_ext_lip.parm b/PARAM/scinter_GB_ext_lip.parm
index e600c30..6b31b91 100644 (file)
--- a/PARAM/scinter_GB_ext_lip.parm
+++ b/PARAM/scinter_GB_ext_lip.parm
@@ -229,7 +229,7 @@
   -0.1779        -3.4493         3.360749       4.211903
    5.240276       3.016734       3.016734
 
-  -6.5557         2.905459       3.641304       4.530360
+  -9.4378         2.905459       3.641304       4.530360
    2.608049       2.608049
 
    2.252800       2.823350       3.512697       2.022197

diff --git a/PARAM/tube.parm b/PARAM/tube.parm
index d3f9616..efae7fd 100644 (file)
--- a/PARAM/tube.parm
+++ b/PARAM/tube.parm
@@ -22,3 +22,7 @@
    6.6424306340
    5.2914044780    
    5.2914044780
+   0.0
+   0.0 
+   0.0
+   0.0

diff --git a/source/cluster/wham/src-M/COMMON.SHIELD b/source/cluster/wham/src-M/COMMON.SHIELD
index 1f96c94..0fb02ed 100644 (file)
--- a/source/cluster/wham/src-M/COMMON.SHIELD
+++ b/source/cluster/wham/src-M/COMMON.SHIELD
@@ -1,10 +1,13 @@
        double precision VSolvSphere,VSolvSphere_div,long_r_sidechain,
      & short_r_sidechain,fac_shield,grad_shield_side,grad_shield,
-     & buff_shield,wshield,grad_shield_loc            
+     & buff_shield,wshield,grad_shield_loc,lipscale,sslipi,sslipj,
+     & ssgradlipi,ssgradlipj 
        integer  ishield_list,shield_list,ees0plist
        common /shield/ VSolvSphere,VSolvSphere_div,buff_shield,
      & long_r_sidechain(ntyp),
      & short_r_sidechain(ntyp),fac_shield(maxres),wshield,
+     & sslipi,sslipj,lipscale,
+     & ssgradlipi,ssgradlipj,
      & grad_shield_side(3,maxcont,-1:maxres),grad_shield(3,-1:maxres),
      &  grad_shield_loc(3,maxcont,-1:maxres),
      & ishield_list(maxres),shield_list(maxcont,maxres),

diff --git a/source/cluster/wham/src-M/energy_p_new.F b/source/cluster/wham/src-M/energy_p_new.F
index dfdaba6..e7759b2 100644 (file)
--- a/source/cluster/wham/src-M/energy_p_new.F
+++ b/source/cluster/wham/src-M/energy_p_new.F
@@ -2349,6 +2349,7 @@ C#undef DEBUG
           el1=el1*fac_shield(i)**2*fac_shield(j)**2
           el2=el2*fac_shield(i)**2*fac_shield(j)**2
           eesij=(el1+el2)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
           ees=ees+eesij
           else
           fac_shield(i)=1.0
@@ -2358,6 +2359,7 @@ C#undef DEBUG
           endif
 C          ees=ees+eesij
           evdw1=evdw1+evdwij*sss
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 cd          write(iout,'(2(2i3,2x),7(1pd12.4)/2(3(1pd12.4),5x)/)')
 cd     &      iteli,i,itelj,j,aaa,bbb,ael6i,ael3i,
 cd     &      1.0D0/dsqrt(rrmij),evdwij,eesij,
@@ -2788,6 +2790,8 @@ C           fac_shield(j)=0.6
           endif
           eel_loc_ij=eel_loc_ij
      &    *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
+
           eel_loc=eel_loc+eel_loc_ij
 C Partial derivatives in virtual-bond dihedral angles gamma
           if (calc_grad) then
@@ -2852,9 +2856,10 @@ cd          write(iout,*) 'aggj1',aggj1
 
 C Derivatives of eello in DC(i+1) thru DC(j-1) or DC(nres-2)
           do l=1,3
-            ggg(l)=agg(l,1)*muij(1)+
-     &          agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4)
+            ggg(l)=(agg(l,1)*muij(1)+
+     &          agg(l,2)*muij(2)+agg(l,3)*muij(3)+agg(l,4)*muij(4))
      &    *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
           enddo
           do k=i+2,j2
@@ -2867,18 +2872,22 @@ C Remaining derivatives of eello
             gel_loc(l,i)=gel_loc(l,i)+aggi(l,1)*muij(1)+
      &          aggi(l,2)*muij(2)+aggi(l,3)*muij(3)+aggi(l,4)*muij(4)
      &    *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
             gel_loc(l,i+1)=gel_loc(l,i+1)+aggi1(l,1)*muij(1)+
      &          aggi1(l,2)*muij(2)+aggi1(l,3)*muij(3)+aggi1(l,4)*muij(4)
      &    *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
             gel_loc(l,j)=gel_loc(l,j)+aggj(l,1)*muij(1)+
      &          aggj(l,2)*muij(2)+aggj(l,3)*muij(3)+aggj(l,4)*muij(4)
      &    *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
             gel_loc(l,j1)=gel_loc(l,j1)+aggj1(l,1)*muij(1)+
      &          aggj1(l,2)*muij(2)+aggj1(l,3)*muij(3)+aggj1(l,4)*muij(4)
      &    *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale+1.0d0)
 
           enddo
           endif
@@ -3178,8 +3187,11 @@ C        fac_shield(j)=0.6
         endif
         eello_turn3=eello_turn3+0.5d0*(pizda(1,1)+pizda(2,2))
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
         eello_t3=0.5d0*(pizda(1,1)+pizda(2,2))
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
 cd        write (2,*) 'i,',i,' j',j,'eello_turn3',
 cd     &    0.5d0*(pizda(1,1)+pizda(2,2)),
@@ -3253,6 +3265,7 @@ C Cartesian derivatives
           gcorr3_turn(l,i)=gcorr3_turn(l,i)
      &      +0.5d0*(pizda(1,1)+pizda(2,2))
      &   *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           a_temp(1,1)=aggi1(l,1)
           a_temp(1,2)=aggi1(l,2)
@@ -3262,6 +3275,7 @@ C Cartesian derivatives
           gcorr3_turn(l,i+1)=gcorr3_turn(l,i+1)
      &      +0.5d0*(pizda(1,1)+pizda(2,2))
      &   *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           a_temp(1,1)=aggj(l,1)
           a_temp(1,2)=aggj(l,2)
@@ -3271,6 +3285,7 @@ C Cartesian derivatives
           gcorr3_turn(l,j)=gcorr3_turn(l,j)
      &      +0.5d0*(pizda(1,1)+pizda(2,2))
      &   *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           a_temp(1,1)=aggj1(l,1)
           a_temp(1,2)=aggj1(l,2)
@@ -3280,6 +3295,7 @@ C Cartesian derivatives
           gcorr3_turn(l,j1)=gcorr3_turn(l,j1)
      &      +0.5d0*(pizda(1,1)+pizda(2,2))
      &   *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
         enddo
         endif
@@ -3333,8 +3349,11 @@ C        fac_shield(j)=0.6
         endif
         eello_turn4=eello_turn4-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+
         eello_t4=-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
 cd        write (2,*) 'i,',i,' j',j,'eello_turn4',-(s1+s2+s3),
 cd     &    ' eello_turn4_num',8*eello_turn4_num
@@ -3390,6 +3409,7 @@ C     &     *2.0
         s3=0.5d0*(pizda(1,1)+pizda(2,2))
         gel_loc_turn4(i)=gel_loc_turn4(i)-(s1+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
 C Derivatives in gamma(i+1)
         call transpose2(EUgder(1,1,i+2),e2tder(1,1))
@@ -3400,6 +3420,7 @@ C Derivatives in gamma(i+1)
         s3=0.5d0*(pizda(1,1)+pizda(2,2))
         gel_loc_turn4(i+1)=gel_loc_turn4(i+1)-(s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
 C Derivatives in gamma(i+2)
         call transpose2(EUgder(1,1,i+3),e3tder(1,1))
@@ -3413,7 +3434,8 @@ C Derivatives in gamma(i+2)
         s3=0.5d0*(pizda(1,1)+pizda(2,2))
         gel_loc_turn4(i+2)=gel_loc_turn4(i+2)-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
-
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
+ 
 C Cartesian derivatives
 C Derivatives of this turn contributions in DC(i+2)
         if (j.lt.nres-1) then
@@ -3434,6 +3456,7 @@ C Derivatives of this turn contributions in DC(i+2)
             ggg(l)=-(s1+s2+s3)
             gcorr4_turn(l,i+2)=gcorr4_turn(l,i+2)-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           enddo
         endif
@@ -3454,6 +3477,7 @@ C Remaining derivatives of this turn contribution
           s3=0.5d0*(pizda(1,1)+pizda(2,2))
           gcorr4_turn(l,i)=gcorr4_turn(l,i)-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           a_temp(1,1)=aggi1(l,1)
           a_temp(1,2)=aggi1(l,2)
@@ -3470,6 +3494,7 @@ C Remaining derivatives of this turn contribution
           s3=0.5d0*(pizda(1,1)+pizda(2,2))
           gcorr4_turn(l,i+1)=gcorr4_turn(l,i+1)-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           a_temp(1,1)=aggj(l,1)
           a_temp(1,2)=aggj(l,2)
@@ -3486,6 +3511,7 @@ C Remaining derivatives of this turn contribution
           s3=0.5d0*(pizda(1,1)+pizda(2,2))
           gcorr4_turn(l,j)=gcorr4_turn(l,j)-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
           a_temp(1,1)=aggj1(l,1)
           a_temp(1,2)=aggj1(l,2)
@@ -3502,6 +3528,7 @@ C Remaining derivatives of this turn contribution
           s3=0.5d0*(pizda(1,1)+pizda(2,2))
           gcorr4_turn(l,j1)=gcorr4_turn(l,j1)-(s1+s2+s3)
      &  *fac_shield(i)*fac_shield(j)
+     &*((sslipi+sslipj)/2.0d0*lipscale**2+1.0d0)
 
         enddo
         endif

diff --git a/source/cluster/wham/src-M/readrtns.F b/source/cluster/wham/src-M/readrtns.F
index 63e0206..21a2b76 100644 (file)
--- a/source/cluster/wham/src-M/readrtns.F
+++ b/source/cluster/wham/src-M/readrtns.F
@@ -208,6 +208,7 @@ C      call reada(weightcard,'WSC',wsc,1.0d0)
       write(iout,*) 'WSHIELD',wshield
       call reada(weightcard,'WTUBE',wtube,0.0d0)
       write(iout,*) 'WTUBE',wtube
+      call reada(weightcard,"LIPSCALE",lipscale,1.3D0)
        call reada(weightcard,'WLT',wliptran,0.0D0)
       call reada(weightcard,"ATRISS",atriss,0.301D0)
       call reada(weightcard,"BTRISS",btriss,0.021D0)
@@ -217,6 +218,10 @@ C      call reada(weightcard,'WSC',wsc,1.0d0)
       write (iout,*) "BTRISS=", btriss
       write (iout,*) "CTRISS=", ctriss
       write (iout,*) "DTRISS=", dtriss
+       if (shield_mode.gt.0) then
+        lipscale=0.0d0
+        write (iout,*) "WARNING:liscale not used in shield mode"
+       endif
       dyn_ss=(index(weightcard,'DYN_SS').gt.0)
       do i=1,maxres
         dyn_ss_mask(i)=.false.

diff --git a/source/unres/src_MD-M/energy_p_new-sep_barrier.F b/source/unres/src_MD-M/energy_p_new-sep_barrier.F
index 44384a6..99b0bc2 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new-sep_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new-sep_barrier.F
@@ -841,7 +841,7 @@ C Calculate gradient components.
               fac=-expon*(e1+evdwij)*rij_shift
               sigder=fac*sigder
               fac=rij*fac
-            fac=fac+evdwij/(1.0-sss)*(-sssgrad)/sigmaii(itypi,itypj)*rij
+            fac=fac+evdwij/sss*(-sssgrad)/sigmaii(itypi,itypj)*rij
 c              fac=0.0d0
 C Calculate the radial part of the gradient
               gg(1)=xj*fac

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 e3a17dd..3703b07 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -3692,13 +3692,13 @@ c        if ((zmedi.gt.((0.5d0)*boxzsize)).or.
 c     &       (zmedi.lt.((-0.5d0)*boxzsize))) then
 c        go to 196
 c        endif
-          xmedi=mod(xmedi,boxxsize)
+          xmedi=dmod(xmedi,boxxsize)
           if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=mod(ymedi,boxysize)
+          ymedi=dmod(ymedi,boxysize)
           if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=mod(zmedi,boxzsize)
+          zmedi=dmod(zmedi,boxzsize)
           if (zmedi.lt.0) zmedi=zmedi+boxzsize
-          zmedi2=mod(zmedi,boxzsize)
+          zmedi2=dmod(zmedi,boxzsize)
           if (zmedi2.lt.0) zmedi2=zmedi2+boxzsize
        if ((zmedi2.gt.bordlipbot)
      &.and.(zmedi2.lt.bordliptop)) then
@@ -3757,11 +3757,11 @@ c     &  .or. itype(i-1).eq.ntyp1
         xmedi=c(1,i)+0.5d0*dxi
         ymedi=c(2,i)+0.5d0*dyi
         zmedi=c(3,i)+0.5d0*dzi
-          xmedi=mod(xmedi,boxxsize)
+          xmedi=dmod(xmedi,boxxsize)
           if (xmedi.lt.0) xmedi=xmedi+boxxsize
-          ymedi=mod(ymedi,boxysize)
+          ymedi=dmod(ymedi,boxysize)
           if (ymedi.lt.0) ymedi=ymedi+boxysize
-          zmedi=mod(zmedi,boxzsize)
+          zmedi=dmod(zmedi,boxzsize)
           if (zmedi.lt.0) zmedi=zmedi+boxzsize
        if ((zmedi.gt.bordlipbot)
      &.and.(zmedi.lt.bordliptop)) then
@@ -3965,6 +3965,7 @@ C lipbufthick is thickenes of lipid buffore
        enddo
        enddo
        if (isubchap.eq.1) then
+C          print *,i,j
           xj=xj_temp-xmedi
           yj=yj_temp-ymedi
           zj=zj_temp-zmedi
@@ -4173,10 +4174,14 @@ C           print *,"bafter", gelc_long(1,i), gelc_long(1,j)
 C Lipidic part for lipscale
             gelc_long(3,j)=gelc_long(3,j)+
      &     ssgradlipj*eesij/2.0d0*lipscale**2
-
+C           if ((ssgradlipj*eesij/2.0d0*lipscale**2).ne.0.0 )
+C     &     write(iout,*) "WTF",j
             gelc_long(3,i)=gelc_long(3,i)+
      &     ssgradlipi*eesij/2.0d0*lipscale**2
 
+C            if ((ssgradlipi*eesij/2.0d0*lipscale**2).ne.0.0 )
+C     &     write(iout,*) "WTF",i
+
 *
 * Loop over residues i+1 thru j-1.
 *

diff --git a/source/unres/src_MD-M/unres.F b/source/unres/src_MD-M/unres.F
index f51b2d7..59c6b64 100644 (file)
--- a/source/unres/src_MD-M/unres.F
+++ b/source/unres/src_MD-M/unres.F
@@ -140,11 +140,11 @@ c      if (me.eq.king .or. .not. out1file) then
 c        write (iout,*) "Calling chainbuild"
 c        call flush(iout)
 c      endif
-      call chainbuild
-c      if (me.eq.king .or. .not. out1file) then
-c        write (iout,*) "Calling MD"
-c        call flush(iout)
-c      endif
+!      call chainbuild
+      if (me.eq.king .or. .not. out1file) then
+        write (iout,*) "Calling MD"
+        call flush(iout)
+      endif
       call MD
       return
       end
@@ -159,9 +159,9 @@ c---------------------------------------------------------------------------
       include 'COMMON.CONTROL'
       include 'COMMON.IOUNITS'
       include 'COMMON.REMD'
-      if (me.eq.king .or. .not. out1file)
-     &   write (iout,*) "Calling chainbuild"
-      call chainbuild
+!      if (me.eq.king .or. .not. out1file)
+!     &   write (iout,*) "Calling chainbuild"
+!      call chainbuild
       if (me.eq.king .or. .not. out1file)
      &   write (iout,*) "Calling REMD"
       if (remd_mlist) then