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
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
enddo
enddo
if (isubchap.eq.1) then
+C print *,i,j
xj=xj_temp-xmedi
yj=yj_temp-ymedi
zj=zj_temp-zmedi
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.
*
#endif
cd write (iout,*) 'i',i,' j',j,' eel_loc_ij',eel_loc_ij
- if (energy_dec) write (iout,'(a6,2i5,0pf7.3)')
- & 'eelloc',i,j,eel_loc_ij
+ if (energy_dec) write (iout,'(a6,2i5,0pf7.3,2f7.3)')
+ & 'eelloc',i,j,eel_loc_ij,a22*muij(1),a23*muij(2)
c if (eel_loc_ij.ne.0)
c & write (iout,'(a4,2i4,8f9.5)')'chuj',
c & i,j,a22,muij(1),a23,muij(2),a32,muij(3),a33,muij(4)
else
do j=1,nbi
diff=vbld(i+nres)-vbldsc0(j,iti)
+ if (energy_dec) write (iout,*)
+ & "estr sc",i,iti,vbld(i+nres),vbldsc0(j,iti),diff,
+ & AKSC(j,iti),AKSC(j,iti)*diff*diff
ud(j)=aksc(j,iti)*diff
u(j)=abond0(j,iti)+0.5d0*ud(j)*diff
enddo
etheta=0.0D0
do i=ithet_start,ithet_end
c print *,i,itype(i-1),itype(i),itype(i-2)
+C if (itype(i-1).eq.ntyp1) cycle
if ((itype(i-1).eq.ntyp1).or.itype(i-2).eq.ntyp1
& .or.itype(i).eq.ntyp1) cycle
C print *,i,theta(i)
esccor=esccor+v1ij*cosphi+v2ij*sinphi
gloci=gloci+j*(v2ij*cosphi-v1ij*sinphi)
enddo
+ if (energy_dec) write(iout,'(a9,2i4,f8.3,3i4)') "esccor",i,j,
+ & esccor,intertyp,
+ & isccori, isccori1
c write (iout,*) "EBACK_SC_COR",i,v1ij*cosphi+v2ij*sinphi,intertyp
gloc_sc(intertyp,i-3,icg)=gloc_sc(intertyp,i-3,icg)+wsccor*gloci
if (lprn)
if ((itype(i).eq.ntyp1).or.(itype(i+1).eq.ntyp1)) cycle
C now calculate distance from center of tube and direction vectors
- vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
- if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
- vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
- if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+C vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+C if (vectube(1).lt.0) vectube(1)=vectube(1)+boxxsize
+C vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+C if (vectube(2).lt.0) vectube(2)=vectube(2)+boxysize
+ xmin=boxxsize
+ ymin=boxysize
+ do j=-1,1
+ vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=vectube(1)+boxxsize*j
+ vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=vectube(2)+boxysize*j
+
+ xminact=abs(vectube(1)-tubecenter(1))
+ yminact=abs(vectube(2)-tubecenter(2))
+ if (xmin.gt.xminact) then
+ xmin=xminact
+ xtemp=vectube(1)
+ endif
+ if (ymin.gt.yminact) then
+ ymin=yminact
+ ytemp=vectube(2)
+ endif
+ enddo
+ vectube(1)=xtemp
+ vectube(2)=ytemp
vectube(1)=vectube(1)-tubecenter(1)
vectube(2)=vectube(2)-tubecenter(2)
rdiff=tub_r-tubeR0
C and its 6 power
rdiff6=rdiff**6.0d0
+C THIS FRAGMENT MAKES TUBE FINITE
+ positi=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+ if (positi.le.0) positi=positi+boxzsize
+C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
+c for each residue check if it is in lipid or lipid water border area
+C respos=mod(c(3,i+nres),boxzsize)
+C print *,positi,bordtubebot,buftubebot,bordtubetop
+ if ((positi.gt.bordtubebot)
+ & .and.(positi.lt.bordtubetop)) then
+C the energy transfer exist
+ if (positi.lt.buftubebot) then
+ fracinbuf=1.0d0-
+ & ((positi-bordtubebot)/tubebufthick)
+C lipbufthick is thickenes of lipid buffore
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
+C print *,ssgradtube, sstube,tubetranene(itype(i))
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+C &+ssgradtube*tubetranene(itype(i))
+C gg_tube(3,i-1)= gg_tube(3,i-1)
+C &+ssgradtube*tubetranene(itype(i))
+C print *,"doing sccale for lower part"
+ elseif (positi.gt.buftubetop) then
+ fracinbuf=1.0d0-
+ &((bordtubetop-positi)/tubebufthick)
+ sstube=sscalelip(fracinbuf)
+ ssgradtube=sscagradlip(fracinbuf)/tubebufthick
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+C gg_tube_SC(3,i)=gg_tube_SC(3,i)
+C &+ssgradtube*tubetranene(itype(i))
+C gg_tube(3,i-1)= gg_tube(3,i-1)
+C &+ssgradtube*tubetranene(itype(i))
+C print *, "doing sscalefor top part",sslip,fracinbuf
+ else
+ sstube=1.0d0
+ ssgradtube=0.0d0
+ enetube(i)=enetube(i)+sstube*tubetranenepep
+C print *,"I am in true lipid"
+ endif
+ else
+C sstube=0.0d0
+C ssgradtube=0.0d0
+ cycle
+ endif ! if in lipid or buffor
+
C for vectorization reasons we will sumup at the end to avoid depenence of previous
- enetube(i)=pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6
+ enetube(i)=enetube(i)+sstube*
+ &(pep_aa_tube/rdiff6**2.0d0+pep_bb_tube/rdiff6)
C write(iout,*) "TU13",i,rdiff6,enetube(i)
C print *,rdiff,rdiff6,pep_aa_tube
C pep_aa_tube and pep_bb_tube are precomputed values A=4eps*sigma^12 B=4eps*sigma^6
C now we calculate gradient
fac=(-12.0d0*pep_aa_tube/rdiff6-
- & 6.0d0*pep_bb_tube)/rdiff6/rdiff
+ & 6.0d0*pep_bb_tube)/rdiff6/rdiff*sstube
C write(iout,'(a5,i4,f12.1,3f12.5)') "TU13",i,rdiff6,enetube(i),
C &rdiff,fac
gg_tube(j,i-1)=gg_tube(j,i-1)+vectube(j)*fac/2.0d0
gg_tube(j,i)=gg_tube(j,i)+vectube(j)*fac/2.0d0
enddo
+ gg_tube(3,i)=gg_tube(3,i)
+ &+ssgradtube*enetube(i)/sstube/2.0d0
+ gg_tube(3,i-1)= gg_tube(3,i-1)
+ &+ssgradtube*enetube(i)/sstube/2.0d0
+
enddo
C basically thats all code now we split for side-chains (REMEMBER to sum up at the END)
C print *,gg_tube(1,0),"TU"
C print *,mod(c(3,i+nres),boxzsize),bordlipbot,bordliptop
c for each residue check if it is in lipid or lipid water border area
C respos=mod(c(3,i+nres),boxzsize)
- print *,positi,bordtubebot,buftubebot,bordtubetop
+C print *,positi,bordtubebot,buftubebot,bordtubetop
+
if ((positi.gt.bordtubebot)
& .and.(positi.lt.bordtubetop)) then
C the energy transfer exist
C lipbufthick is thickenes of lipid buffore
sstube=sscalelip(fracinbuf)
ssgradtube=-sscagradlip(fracinbuf)/tubebufthick
- print *,ssgradtube, sstube,tubetranene(itype(i))
+C print *,ssgradtube, sstube,tubetranene(itype(i))
enetube(i+nres)=enetube(i+nres)+sstube*tubetranene(itype(i))
C gg_tube_SC(3,i)=gg_tube_SC(3,i)
C &+ssgradtube*tubetranene(itype(i))
zmin=boxzsize
do j=-1,1
- vectube(1)=mod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
+ vectube(1)=dmod((c(1,i)+c(1,i+1))/2.0d0,boxxsize)
vectube(1)=vectube(1)+boxxsize*j
- vectube(2)=mod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
+ vectube(2)=dmod((c(2,i)+c(2,i+1))/2.0d0,boxysize)
vectube(2)=vectube(2)+boxysize*j
- vectube(3)=mod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
+ vectube(3)=dmod((c(3,i)+c(3,i+1))/2.0d0,boxzsize)
vectube(3)=vectube(3)+boxzsize*j
- xminact=abs(vectube(1)-tubecenter(1))
- yminact=abs(vectube(2)-tubecenter(2))
- zminact=abs(vectube(3)-tubecenter(3))
+ xminact=dabs(vectube(1)-tubecenter(1))
+ yminact=dabs(vectube(2)-tubecenter(2))
+ zminact=dabs(vectube(3)-tubecenter(3))
if (xmin.gt.xminact) then
xmin=xminact
enecavtube(i)=0.0
faccav=0.0
else
- denominator=(1.0+dcavtubpep*rdiff6*rdiff6)
+ denominator=(1.0d0+dcavtubpep*rdiff6*rdiff6)
enecavtube(i)=
- & (bcavtubpep*rdiff+acavtubpep*sqrt(rdiff)+ccavtubpep)
+ & (bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)+ccavtubpep)
& /denominator
enecavtube(i)=0.0
- faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/sqrt(rdiff))
- & *denominator-(bcavtubpep*rdiff+acavtubpep*sqrt(rdiff)
+ faccav=((bcavtubpep*1.0d0+acavtubpep/2.0d0/dsqrt(rdiff))
+ & *denominator-(bcavtubpep*rdiff+acavtubpep*dsqrt(rdiff)
& +ccavtubpep)*rdiff6**2.0d0/rdiff*dcavtubpep*12.0d0)
& /denominator**2.0d0
C faccav=0.0
enddo
do i=itube_start,itube_end
- enecavtube(i)=0.0
+ enecavtube(i)=0.0d0
C Lets not jump over memory as we use many times iti
iti=itype(i)
C lets ommit dummy atoms for now
ymin=boxysize
zmin=boxzsize
do j=-1,1
- vectube(1)=mod((c(1,i+nres)),boxxsize)
+ vectube(1)=dmod((c(1,i+nres)),boxxsize)
vectube(1)=vectube(1)+boxxsize*j
- vectube(2)=mod((c(2,i+nres)),boxysize)
+ vectube(2)=dmod((c(2,i+nres)),boxysize)
vectube(2)=vectube(2)+boxysize*j
- vectube(3)=mod((c(3,i+nres)),boxzsize)
+ vectube(3)=dmod((c(3,i+nres)),boxzsize)
vectube(3)=vectube(3)+boxzsize*j
- xminact=abs(vectube(1)-tubecenter(1))
- yminact=abs(vectube(2)-tubecenter(2))
- zminact=abs(vectube(3)-tubecenter(3))
+ xminact=dabs(vectube(1)-tubecenter(1))
+ yminact=dabs(vectube(2)-tubecenter(2))
+ zminact=dabs(vectube(3)-tubecenter(3))
if (xmin.gt.xminact) then
xmin=xminact
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+nres)=0.0
- faccav=0.0
+ enecavtube(i+nres)=0.0d0
+ faccav=0.0d0
else
- denominator=(1.0+dcavtub(iti)*rdiff6*rdiff6)
+ denominator=(1.0d0+dcavtub(iti)*rdiff6*rdiff6)
enecavtube(i+nres)=
- & (bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)+ccavtub(iti))
+ & (bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)+ccavtub(iti))
& /denominator
C enecavtube(i)=0.0
- faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/sqrt(rdiff))
- & *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*sqrt(rdiff)
+ faccav=((bcavtub(iti)*1.0d0+acavtub(iti)/2.0d0/dsqrt(rdiff))
+ & *denominator-(bcavtub(iti)*rdiff+acavtub(iti)*dsqrt(rdiff)
& +ccavtub(iti))*rdiff6**2.0d0/rdiff*dcavtub(iti)*12.0d0)
& /denominator**2.0d0
C faccav=0.0
projects / unres.git / blobdiff