introcuction of cavity term for pepgroup for nanosphere

diff --git a/PARAM/TiO2_fin.parm b/PARAM/TiO2_fin.parm
index c8a2d74..3a77d65 100644 (file)
--- a/PARAM/TiO2_fin.parm
+++ b/PARAM/TiO2_fin.parm
@@ -1,4 +1,4 @@
-   0.058   4.710                                            0.00 ! Pep
+  3.929   3.894  -241.329    50.844   288.017   6.165E-10 0.0 ! Pep
   0.174   4.496     2.222    -0.393    -3.104  -1.392E-12 0.0 ! Cys 
   4.173   4.136  -143.035    28.494   180.705   1.086E-10 0.0 ! Met 
  10.793   4.152  -250.420    48.235   328.091   7.237E-11 0.0 ! Phe 

diff --git a/source/unres/src_MD-M/COMMON.INTERACT b/source/unres/src_MD-M/COMMON.INTERACT
index f94a51b..f7ba255 100644 (file)
--- a/source/unres/src_MD-M/COMMON.INTERACT
+++ b/source/unres/src_MD-M/COMMON.INTERACT
@@ -1,6 +1,7 @@
       double precision aa,bb,augm,aad,bad,app,bpp,ale6,ael3,ael6,
      &aa_lip,bb_lip,aa_aq,bb_aq,sc_aa_tube_par,sc_bb_tube_par,
-     & pep_aa_tube,pep_bb_tube,dcavtub,acavtub,bcavtub,ccavtub
+     & pep_aa_tube,pep_bb_tube,dcavtub,acavtub,bcavtub,ccavtub,
+     & dcavtubpep,acavtubpep,bcavtubpep,ccavtubpep
       double precision wdti,wdti2,wdti4,wdti8,
      &                 wdtii,wdtii2,wdtii4,wdtii8 
       common /nosehoover_dt/
@@ -16,7 +17,8 @@
      & aa_lip(ntyp,ntyp),bb_lip(ntyp,ntyp),
      & sc_aa_tube_par(ntyp),sc_bb_tube_par(ntyp),
      & pep_aa_tube,pep_bb_tube,acavtub(ntyp),dcavtub(ntyp),
-     & bcavtub(ntyp),ccavtub(ntyp),
+     & bcavtub(ntyp),ccavtub(ntyp),acavtubpep,dcavtubpep,
+     & bcavtubpep,ccavtubpep,
      & augm(ntyp,ntyp),
      & aad(ntyp,2),bad(ntyp,2),app(2,2),bpp(2,2),ael6(2,2),ael3(2,2),
      & expon,expon2,nnt,nct,nint_gr(maxres),istart(maxres,maxint_gr),

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 c037ff3..91a7c94 100644 (file)
--- a/source/unres/src_MD-M/energy_p_new_barrier.F
+++ b/source/unres/src_MD-M/energy_p_new_barrier.F
@@ -12589,7 +12589,30 @@ C now we calculate gradient
      &       6.0d0*pep_bb_tube)/rdiff6/rdiff
 C       write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
 C     &rdiff,fac
-
+         if (acavtubpep.eq.0.0d0) then
+C go to 667
+         enecavtube(i)=0.0
+         faccav=0.0
+         else
+         denominator=(1.0+dcavtubpep*rdiff6*rdiff6)
+         enecavtube(i)=
+     &   (bcavtubpep*rdiff+acavtubpep*sqrt(rdiff)+ccavtubpep)
+     &   /denominator
+         enecavtube(i)=0.0
+         faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/sqrt(rdiff))
+     &   *denominator-(bcavtubpep*rdiff+acavtubpep*sqrt(rdiff)
+     &   +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0)
+     &   /denominator**2.0d0
+C         faccav=0.0
+C         fac=fac+faccav
+C 667     continue
+         endif
+C         print *,"TUT",i,iti,rdiff,rdiff6,acavtubpep,denominator,
+C     &   enecavtube(i),faccav
+C         print *,"licz=",
+C     & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+CX         print *,"finene=",enetube(i+nres)+enecavtube(i)
+         
 C now direction of gg_tube vector
         do j=1,3
         gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
@@ -12669,11 +12692,11 @@ C now direction of gg_tube vector
 C Now cavity term E=a(x+bsqrt(x)+c)/(1+dx^12)
          if (acavtub(iti).eq.0.0d0) then
 C go to 667
-         enecavtube(i)=0.0
+         enecavtube(i+nres)=0.0
          faccav=0.0
          else
          denominator=(1.0+dcavtub(iti)*rdiff6*rdiff6)
-         enecavtube(i)=
+         enecavtube(i+nres)=
      &   (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
      &   /denominator
 C         enecavtube(i)=0.0
@@ -12685,11 +12708,11 @@ C         faccav=0.0
          fac=fac+faccav
 C 667     continue
          endif
-         print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator,
-     &   enecavtube(i),faccav
-         print *,"licz=",
-     & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
-         print *,"finene=",enetube(i+nres)+enecavtube(i)
+C         print *,"TUT",i,iti,rdiff,rdiff6,acavtub(iti),denominator,
+C     &   enecavtube(i),faccav
+C         print *,"licz=",
+C     & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+C         print *,"finene=",enetube(i+nres)+enecavtube(i)
          do j=1,3
           gg_tube_SC(j,i)=gg_tube_SC(j,i)+vectube(j)*fac
           gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac
@@ -12705,6 +12728,7 @@ C        if (acavtub(iti).eq.0.0) cycle
 
         do i=itube_start,itube_end
           Etube=Etube+enetube(i)+enetube(i+nres)+enecavtube(i)
+     & +enecavtube(i+nres)
         enddo
 C        print *,"ETUBE", etube
         return

diff --git a/source/unres/src_MD-M/parmread.F b/source/unres/src_MD-M/parmread.F
index b80095b..78d0afb 100644 (file)
--- a/source/unres/src_MD-M/parmread.F
+++ b/source/unres/src_MD-M/parmread.F
@@ -1361,7 +1361,8 @@ c           augm(i,j)=0.5D0**(2*expon)*aa(i,j)
         enddo
       enddo
       write(iout,*) "tube param"
-      read(itube,*) epspeptube,sigmapeptube,tubetranenepep
+      read(itube,*) epspeptube,sigmapeptube,acavtubpep,bcavtubpep,
+     & ccavtubpep,dcavtubpep,tubetranenepep
       sigmapeptube=sigmapeptube**6
       sigeps=dsign(1.0D0,epspeptube)
       epspeptube=dabs(epspeptube)