From 9a26354af2c68a12347d7f85ad158e3ba22fdd7d Mon Sep 17 00:00:00 2001 From: Adam Sieradzan Date: Tue, 21 Feb 2017 11:54:23 +0100 Subject: [PATCH] introcuction of cavity term for pepgroup for nanosphere --- PARAM/TiO2_fin.parm | 2 +- source/unres/src_MD-M/COMMON.INTERACT | 6 ++-- source/unres/src_MD-M/energy_p_new_barrier.F | 40 ++++++++++++++++++++------ source/unres/src_MD-M/parmread.F | 3 +- 4 files changed, 39 insertions(+), 12 deletions(-) diff --git a/PARAM/TiO2_fin.parm b/PARAM/TiO2_fin.parm index c8a2d74..3a77d65 100644 --- 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 --- 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 --- 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 --- 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) -- 1.7.9.5