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knot99bp_LJconf.f
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program brownian
implicit double precision(a-h,o-z)
parameter ( men=99 )
common/pos/x0(men),y0(men),z0(men)
common/vel/x1(men),y1(men),z1(men)
common/for/fx(men),fy(men),fz(men)
common/prop/sumv,xsum,isum
common/sig/sigma(men,men),sigma0,cut1,cut2,eshift
common/bon/bond,H1,H2,b(men-1)
common/nat/xn(men),yn(men),zn(men)
COMMON/SAMPLE/ETA(men,men),CR(men,men)
COMMON/PARA/CK,AR0,ALPHA
COMMON/MONO/N
common/cle/kb
common/cutoff/rcut
character*100 fname1,fname2,fname3,residue*2,residuename*5
dimension aaa(100),dis_b(men)
common/force/fstr
residue=" P"
residuename=" C"
nchain=1
fstr=0.000
c tr=0.125d0
part=men
N=men
write(fname1,"(a,f5.3,a)")
&'thermo_',fstr,'_99bp_dt0.01_topo_endfree.dat'
open(14,file=fname1,status='unknown')
write(fname3,'(a,f5.3,a)')
&'dishb_',fstr,'_99bp_dt0.01_topo_endfree.dat'
open(15,file=fname3,status='unknown')
rcut=1.122d0
! SET PARAMETERS
CK=100.0d0 !! ELASTIC CONSTANT
AR0=1.122d0 !! MINIMUM POSITION OF THE L-J POTENTIAL
ALPHA=0.0d0
iflg = 0 ! save to 'simdata.kat' when iflg=1
c CALL GOSAMPLE
open(20,file='trefoil_short_loose.txt',status='old')
DO I=1,men
read(20,*)xn(i),yn(i),zn(i)
x0(i)=xn(i)
y0(i)=yn(i)
z0(i)=zn(i)
ENDDO
close(20)
CALL FORENER(AVCF,ENER)
! READ PARAMETERS FROM FILE
open(1,file='test1.inp',status='old')
read(1,*)H1
read(1,*)H2
c read(1,*)tr
read(1,*)delta
read(1,*)GAMMA
read(1,*)maxkb
read(1,*)nconf
read(1,*)kflg
read(1,*)istart
read(1,*)kwrite
read(1,*)dfold
read(1,*)ieq
read(1,*)icq
close(1)
open(2, file='seed.inp', status='old')
read(2,*)iseed
close(2)
! SET PARAMETERS IN PREDICTOR-CORRECTOR METHOD
DeltEuler=delta/GAMMA
! SCALE FACTORS FOR VELOCITIES DURING EQUILIBRATION
pi=3.14159265d0
twopi=8.d0*datan(1.d0)
delsq=delta*delta
deltsq=0.5d0*delsq
! LANGEVIN PARAMETERS
xmass=1.d0
aaa(1)=0.200d0
aaa(2)=0.205d0
aaa(3)=0.210d0
aaa(4)=0.215d0
aaa(5)=0.220d0
aaa(6)=0.225d0
aaa(7)=0.230d0
aaa(8)=0.235d0
aaa(9)=0.240d0
aaa(10)=0.245d0
aaa(11)=0.250d0
aaa(12)=0.255d0
aaa(13)=0.260d0
aaa(14)=0.265d0
aaa(15)=0.270d0
aaa(16)=0.275d0
aaa(17)=0.280d0
aaa(18)=0.285d0
aaa(19)=0.290d0
aaa(20)=0.295d0
c iseed=674673
dfr=rand(iseed)
loop=1.0
c open(3, file='status.txt', status='unknown')
do ii=10,10
tr=aaa(ii)
c write(3,*)tr
write(fname2,'(a,f5.3,a,f5.3,a)')
&'traj_',fstr,'_',tr,'_99bp_dt0.005_topo_endfree.dat'
open(13,file=fname2,status='unknown')
write(13,*)nchain
write(13,*)men
do i=1,men
write(13,"(I4,a2,a5)")i,residue !,residuename
enddo
write(13,"(I10)")men
aheat=delsq*part*3*tr
const2=2.d0*tr*gamma/(delta*xmass)
const2=dsqrt(const2)
! LOAD INITIAL VELOCITIES OF PARTICLES
call Intvel3d(aheat,part)
CALL brownianforce(twopi,const2)
time=0.d0
tmp=tr
ekin=part*tr
etot=epot+ekin
call tempe(part,delta,tmpins)
c -----------------------------------------
c ENTER MAIN LOOP OF SIMULATION
c -----------------------------------------
kb=0
sume=0.d0
sume2=0.d0
do ic=1,men/2
dis_b(ic)=0.0d0
enddo
533 continue
kb=kb+1
CALL FORENER(AVCF,epot)
call brownianforce(twopi,const2)
do 37 i=1,men
if(i.eq.1.or.i.eq.men) goto 37
x0(i)=x0(i)+DeltEuler*fx(i)
y0(i)=y0(i)+DeltEuler*fy(i)
z0(i)=z0(i)+DeltEuler*fz(i)
37 continue
if(kb.gt.ieq)then
sume=sume+epot
sume2=sume2+epot*epot
endif
call tempe(part,delta,tmpins) ! Instant. Temp.
c Call CPU_time(t2)
c if((kb.gt.ieq).and.(kb/1000)*1000.eq.kb)then
if((kb/1000)*1000.eq.kb)then
write(13,*)kb
do ik=1,men
write(13,"(3f13.3)")x0(ik),y0(ik),z0(ik)
enddo
if(kb.lt.maxkb)then
write(13,*)'continue'
endif
endif
if(kb.gt.ieq)then
nb=0
do ib1=1,men/2
do ib2=((men/2)+1), men
c do ib2=men/2+1, MEN
if((ib1+ib2).eq.(men+1))then
nb=nb+1
dx=x0(ib1)-x0(ib2)
dy=y0(ib1)-y0(ib2)
dz=z0(ib1)-z0(ib2)
r=sqrt(dx**2+dy**2+dz**2)
dis_b(nb)=dis_b(nb)+r
endif
enddo
enddo
endif
if(kb.le.maxkb)goto 533
c Call System("bzip2 " // fname2)
avge=sume/(maxkb-ieq)
avge2=sume2/(maxkb-ieq)
avgn=cont/(maxkb-ieq)
fluc=avge2-avge**2
write(14,"(4f15.5)")fstr,tr,avge,(fluc/(tr**2))
c write(3,"(4f15.5)")fstr,tr,avge,(fluc/(tr**2))
c Call CPU_time(t2)
c write(*,*)kb,t2
do ik1=1,men/2
write(15,"(f6.3,I4,f10.3)")tr,ik1,dis_b(ik1)/(maxkb-ieq)
c write(*,"(f6.3,I4,f10.3)")tr,ik1,dis_b(ik1)/(maxkb-ieq)
enddo
close(13)
enddo
close(14)
close(15)
c close (3)
! END LOOP OF SIMULATION
! END OF EXECUTION
end
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
subroutine intvel3d(aheat,part)
implicit double precision(a-h,o-z)
! ASSIGN INITIAL VELOCITIES TO ATOMS
parameter ( men=99 )
common/vel/x1(men),y1(men),z1(men)
sumx=0.
sumy=0.
sumz=0.
do 200 i=1,men
c if(i.eq.1.or.i.eq.(MEN/2).or.i.eq.((MEN/2)+1).or.i.eq.MEN)goto 200
xx=2.d0*(rand(0)-0.5d0)
yy=2.d0*(rand(0)-0.5d0)
zz=2.d0*(rand(0)-0.5d0)
xyz=1.d0/ dsqrt(xx*xx+yy*yy+zz*zz)
x1(i)=xx*xyz
y1(i)=yy*xyz
z1(i)=zz*xyz
sumx=sumx+x1(i)
sumy=sumy+y1(i)
sumz=sumz+z1(i)
200 continue
! SCALE VELOCITIES SO THAT TOTAL MOMENTUM = ZERO
x=0.d0
do 210 i=1,men
c if(i.eq.1.or.i.eq.(men/2).or.i.eq.((men/2)+1).or.i.eq.men)goto 210
x1(i)=x1(i)-sumx/part
y1(i)=y1(i)-sumy/part
z1(i)=z1(i)-sumz/part
x=x+x1(i)*x1(i)+y1(i)*y1(i)+z1(i)*z1(i)
210 continue
! SCALE VELOCITIES TO DESIRED TEMPERATURE
heat= dsqrt(aheat/x)
do 220 i=1,men
c if(i.eq.1.or.i.eq.(men/2).or.i.eq.((men/2)+1).or.i.eq.men)goto 220
x1(i)=x1(i)*heat
y1(i)=y1(i)*heat
z1(i)=z1(i)*heat
220 continue
return
end
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
subroutine brownianforce(twopi,const2)
implicit double precision(a-h,o-z)
parameter(men= 99)
common/vel/x1(men),y1(men),z1(men)
common/for/fx(men),fy(men),fz(men)
common/cle/kb
common/cutoff/rcut
do 26 i=1,men
c if(i.eq.1.or.i.eq.(MEN/2).or.i.eq.((MEN/2)+1).or.i.eq.MEN)goto 26
101 r1=rand(0)
r2=rand(0)
r3=rand(0)
r4=rand(0)
r5=rand(0)
r6=rand(0)
if(r1.eq.0.or.r2.eq.0.or.r3.eq.0.or.r4.eq.0.or.r5.eq.0.or.
&r6.eq.0)goto 101
gam1=dsqrt(-2.d0*log(r1))*dcos(twopi*r2)
gam2=dsqrt(-2.d0*log(r3))*dcos(twopi*r4)
gam3=dsqrt(-2.d0*log(r5))*dcos(twopi*r6)
fx(i)=fx(i)+const2*gam1 !gamma*delta
fy(i)=fy(i)+const2*gam2
fz(i)=fz(i)+const2*gam3
26 continue
return
end
c-------------------------------------------------------------------
subroutine tempe(part,delta,tmpins)
implicit double precision(a-h,o-z)
parameter(men=99)
common/vel/x1(men),y1(men),z1(men)
! Center of Mass
vxcm=0.d0
vycm=0.d0
vzcm=0.d0
do i=1,men
vxcm=vxcm+x1(i)
vycm=vycm+y1(i)
vzcm=vzcm+z1(i)
enddo
anorm=1.d0/part
vxcm=vxcm*anorm
vycm=vycm*anorm
vzcm=vzcm*anorm
! Directional instantaneous temperatures
sumvelx=0.d0
sumvely=0.d0
sumvelz=0.d0
do i=1,men
x=x1(i)-vxcm ! center of mass subtracted
y=y1(i)-vycm
z=z1(i)-vzcm
sumvelx=sumvelx + x*x
sumvely=sumvely + y*y
sumvelz=sumvelz + z*z
enddo
anorm = 1.d0/(part*delta*delta)
tmpx=sumvelx*anorm
tmpy=sumvely*anorm
tmpz=sumvelz*anorm
tmpins = (tmpx+tmpy+tmpz)/3
return
end
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
SUBROUTINE FORENER(AVCF,ENER)
IMPLICIT DOUBLE PRECISION(A-H,O-Z)
PARAMETER (men=99)
DIMENSION CX(men),CY(men)
DIMENSION CFX(20),CFY(20)
common/pos/x0(men),y0(men),z0(men)
common/for/fx(men),fy(men),fz(men)
COMMON/SAMPLE/ETA(men,men),CR(men,men)
COMMON/PARA/CK,AR0,ALPHA
COMMON/MONO/N
common/force/fstr
common/cle/kb
common/cutoff/rcut
ENER=0.d0
do i=1,men
fx(i) = 0.d0
fy(i) = 0.d0
fz(i) = 0.d0
enddo
do 495 i=1,men-1
xi=x0(i)
yi=y0(i)
zi=z0(i)
do 496 j=i+1,men
dx = xi-x0(j)
dy = yi-y0(j)
dz = zi-z0(j)
rsq=dx*dx+dy*dy+dz*dz
r = dsqrt(rsq)
IF(J.EQ.(I+1))THEN !! HARMONIC PART
FCE=-2*CK*(R-AR0)/R
ENE=CK*(R-AR0)**2
ELSE !! L-J PART
c if((i.eq.1.and.j.eq.(men/2)).or.
c &(i.eq.((men/2)+1).and.j.eq.men))then
c FCE=-2*CK*(R-1.12d0)/R
c ENE=CK*(R-1.12d0)**2
c goto 775
c endif
if(r.gt.rcut)goto 496
c if(i.eq.18.and.j.eq.19)then
c write(*,*)i,j, CR(I,J), ETA(I,J)
c pause
c endif
AA=1/RSQ**6
BB=1/RSQ**3
ENE=4.0d0*(AA-BB+0.25)
FCE=48.0d0*AA-24.0d0*BB
FCE=FCE/RSQ
ENDIF
775 continue
c if(kb.ge.5503.and.kb.le.5505)then
c write(*,*)FCE
c endif
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
repx=fce*dx
repy=fce*dy
repz=fce*dz
fx(i) = fx(i) + repx
fx(j) = fx(j) - repx
fy(i) = fy(i) + repy
fy(j) = fy(j) - repy
fz(i) = fz(i) + repz
fz(j) = fz(j) - repz
ENER=ENER+ENE
496 continue
495 continue
c wall force
do 613 i=5,men-4
dy1=y0(i)-y0(1)
dy2=y0(men)-y0(i)
c write(*,*) i, x0(i), x0(1), x0(men)
if (dy1.lt.rcut) then
AA=1/dy1**12
BB=1/dy1**6
ENE=4.0d0*(AA-BB)
ENER=ENER+ENE
FCE=48.0d0*AA-24.0d0*BB
fy(i)=fy(i)+FCE
c write(*,*) FCE, ENE, i, dy1
else if (dy2.lt.rcut) then
AA=1/dy2**12
BB=1/dy2**6
ENE=4.0d0*(AA-BB)
ENER=ENER+ENE
FCE=48.0d0*AA-24.0d0*BB
fy(i)=fy(i)-FCE
c write(*,*) FCE, ENE, i, dy2
endif
613 continue
C external force
if(y0(1).gt.y0(men))then
fy(1)=fy(1)+fstr
fy(men)=fy(men)-fstr
else
fy(1)=fy(1)-fstr
fy(men)=fy(men)+fstr
endif
C CALCULATE AVERAGE FORCE F
AVCF=0.D0
DO 782 I=1,N
AVCF=AVCF+(FX(I)**2+FY(I)**2+FZ(I)**2)
782 CONTINUE
AVCF=DSQRT(AVCF)/N
RETURN
END
ccc-------------------------------------------------------------
SUBROUTINE GOSAMPLE
IMPLICIT DOUBLE PRECISION(A-H,O-Z)
PARAMETER(men=99)
COMMON/SAMPLE/ETA(men, men),CR(men, men)
COMMON/PARA/CK,AR0,ALPHA
COMMON/MONO/N
DO I=1,N-1
DO J=I+1,N
IF(J.EQ.(I+1).and.j.ne.((men/2)+1))THEN
ETA(I,J)=0.D0
CR(I,J)=0.D0
ELSE
if((i+j).eq.(men+1))then
ETA(I,J)=1.D0 !!! ALPHA=0.
CR(I,J)=1.D0
else
ETA(I,J)=ALPHA !!! ALPHA=0.
CR(I,J)=1.D0
endif
c pause
ENDIF
ENDDO
ENDDO
C PUT NONZERO NATIVE CONTACT ENERGIES FOR TARGET (CELL 63)
DO I=1,N-1
DO J=I+1,N
ETA(J,I)=ETA(I,J)
CR(J,I)=CR(I,J) !!!! SYMMETRY
ENDDO
ENDDO
RETURN
END