********>Bugfix 13:
Author: Ross Walker, with help from Bing Wang and Dave Case
Date: 06/18/2004
Programs: sander.QMMM
Description: Several patches are needed to make the QMMM option work
correctly, especially for molecular dynamics. These involve
glitches in transfering things from the ROAR environment to
sander.
Fix: save this file to bugfix.13
cd $AMBERHOME
patch -N -p0 -r rejects < bugfix.13
------------------------------------------------------------------------------
*** src/sander/dynlib.f 2004/06/18 15:51:52 7.70
--- src/sander/dynlib.f 2004/06/18 16:01:09
***************
*** 316,322 ****
--- 316,327 ----
else
write(6,9059) eel,ehbond,econst
end if
+ #ifdef QMMM
+ !write the SCF energy
+ write(6,9080) esurf
+ #else
if (gbsa > 0) write(6,9077) esurf
+ #endif
if (econst /= 0.0) write(6,9076) epot-econst
if ( dvdl /= 0.d0) write(6,9089) dvdl
#ifndef LES
***************
*** 367,373 ****
--- 372,383 ----
else
write(7,9059) eel,ehbond,econst
end if
+ #ifdef QMMM
+ !write the SCF energy
+ write(7,9080) esurf
+ #else
if (gbsa > 0) write(7,9077) esurf
+ #endif
if (econst /= 0.0) write(7,9076) epot-econst
if ( dvdl /= 0.d0) write(7,9089) dvdl
#ifndef LES
***************
*** 411,416 ****
--- 421,427 ----
9078 format (1x,'EKCMT = ',f14.4,2x,'VIRIAL = ',f14.4,2x, &
'VOLUME = ',f14.4)
9079 format (52x,'Density = ',f14.4)
+ 9080 format (1x,'ESCF = ',f14.4)
#ifdef LES
! LES and non-LES temperatures (no solvent/solute)
*** src/sander/link_atoms.f 2003/12/31 21:19:23 7.5
--- src/sander/link_atoms.f 2004/06/18 16:01:51
***************
*** 1,5 ****
subroutine link_atoms(nbonds,x,nlink,npert,ib,jb, &
! qmlink,nquant,labels,natoms,winv,numbon,mmqmbo, &
igrp)
!
implicit double precision (a-h,o-z)
--- 1,5 ----
subroutine link_atoms(nbonds,x,nlink,npert,ib,jb, &
! qmlink,nquant,labels,natoms,winv,amass,numbon,mmqmbo, &
igrp)
!
implicit double precision (a-h,o-z)
***************
*** 9,15 ****
! common/parms/rk(5000),req(5000),tk(900),teq(900),pk(900),pn(900),
! + phase(900),cn1(1830),cn2(1830),solty(60),
! + gamc(900),gams(900),ipn(900),fmn(900)
! dimension x(*),ib(*),jb(*),qmlink(*),labels(*),winv(*)
dimension mmqmbo(*),igrp(*)
!
! PMF info:
--- 9,15 ----
! common/parms/rk(5000),req(5000),tk(900),teq(900),pk(900),pn(900),
! + phase(900),cn1(1830),cn2(1830),solty(60),
! + gamc(900),gams(900),ipn(900),fmn(900)
! dimension x(*),ib(*),jb(*),qmlink(*),labels(*),winv(*),amass(*)
dimension mmqmbo(*),igrp(*)
!
! PMF info:
***************
*** 82,91 ****
150 continue
nlink = mm
end if
! do 200 i=1,nlink
! winv(i) = atinv
! igrp(i) = 1
! 200 continue
!
! identify those atoms directly bonded to quantum atoms
!
--- 82,92 ----
150 continue
nlink = mm
end if
! do i=1,nlink
! winv(i) = atinv
! amass(i) = 1.d0/atinv
! igrp(i) = 1
! end do
!
! identify those atoms directly bonded to quantum atoms
!
*** src/sander/locmem.f 2004/03/14 06:07:35 7.116
--- src/sander/locmem.f 2004/06/18 16:02:58
***************
*** 205,211 ****
! --- real array NMR restraints/weight changes:
! call adj_mem_ptr( r_ptr, lmass, natom )
call adj_mem_ptr( r_ptr, lnmr01, irlreq )
call adj_mem_ptr( r_ptr, l75, natom )
--- 205,211 ----
! --- real array NMR restraints/weight changes:
! call adj_mem_ptr( r_ptr, lmass, natom + ncpp )
call adj_mem_ptr( r_ptr, lnmr01, irlreq )
call adj_mem_ptr( r_ptr, l75, natom )
***************
*** 214,220 ****
--- 214,228 ----
else if (nmropt > 0 ) then
call adj_mem_ptr( r_ptr, l95, max(natom, 2*ntbond) )
else
+ #ifdef QMMM
+ ! QMMM code uses l95 as xwij(3,ln) in resnba. The memory allocated
+ ! to this used to be much bigger in the amber 4.1 days and so we
+ ! need to make sure it is big enough for use in the old nonbond
+ ! list code.
+ call adj_mem_ptr( r_ptr, l95, max(3*nmxrs*nmxrs,2*ntbond) )
+ #else
call adj_mem_ptr( r_ptr, l95, 2*ntbond )
+ #endif
end if
if( igb /= 0 ) then
call adj_mem_ptr( r_ptr, l96, natom )
***************
*** 323,329 ****
call adj_mem_ptr( i_ptr, i02, nres + 1 )
call adj_mem_ptr( i_ptr, i04, natom+ncpp )
call adj_mem_ptr( i_ptr, i06, ntypes*ntypes )
! call adj_mem_ptr( i_ptr, i08, natom+ncpp )
call adj_mem_ptr( i_ptr, i10, 2*nnb )
iibh = i_ptr
--- 331,337 ----
call adj_mem_ptr( i_ptr, i02, nres + 1 )
call adj_mem_ptr( i_ptr, i04, natom+ncpp )
call adj_mem_ptr( i_ptr, i06, ntypes*ntypes )
! call adj_mem_ptr( i_ptr, i08, natom + ncpp )
call adj_mem_ptr( i_ptr, i10, 2*nnb )
iibh = i_ptr
*** src/sander/rdparm.f 2004/06/15 21:08:03 7.75
--- src/sander/rdparm.f 2004/06/18 16:03:39
***************
*** 207,222 ****
left = natom - (num*20)
kk = 1
mm = 1
if(num.ge.1) then
do i=1,num
cstrng(:) = ' '
ll = 1
- FMTIN = AFMT
- TYPE = 'ATOM_NAME'
- CALL NXTSEC(NF, 6, 0,FMTIN, TYPE, FMT, IOK)
- do jtemp = 1, i-1
- read(nf,9108)
- enddo
read(nf,9138)(cstrng(k),k=1,80)
call qmcompare(cstrng,itemp,20)
do n=1,20
--- 207,219 ----
left = natom - (num*20)
kk = 1
mm = 1
+ FMTIN = AFMT
+ TYPE = 'ATOM_NAME'
+ CALL NXTSEC(NF, 6, 0,FMTIN, TYPE, FMT, IOK)
if(num.ge.1) then
do i=1,num
cstrng(:) = ' '
ll = 1
read(nf,9138)(cstrng(k),k=1,80)
call qmcompare(cstrng,itemp,20)
do n=1,20
***************
*** 237,259 ****
ll = 1
read(nf,9138)(cstrng(k),k=1,80)
call qmcompare(cstrng,itemp,left)
! if(left.eq.1) then
if(labels(kk).eq.mm) then
! mlabel(kk) = itemp(1)
end if
! else
! do n=1,left
! if(labels(kk).eq.mm) then
! mlabel(kk) = itemp(ll)
! mm = mm + 1
! ll = ll + 1
! kk = kk + 1
! else
! mm = mm + 1
! ll = ll + 1
! end if
! end do
! end if
end if
end if
#endif
--- 234,250 ----
ll = 1
read(nf,9138)(cstrng(k),k=1,80)
call qmcompare(cstrng,itemp,left)
! do n=1,left
if(labels(kk).eq.mm) then
! mlabel(kk) = itemp(ll)
! mm = mm + 1
! ll = ll + 1
! kk = kk + 1
! else
! mm = mm + 1
! ll = ll + 1
end if
! end do
end if
end if
#endif
*** src/sander/runmd.f 2004-06-18 13:37:28.000000000 -0700
--- src/sander/runmd.f 2004-06-18 13:37:43.000000000 -0700
***************
*** 185,194 ****
lout = .true.
loutfm = ioutfm <= 0
nr = nrp
- nr3 = 3*nr
#ifdef QMMM
nr = nr + nlink
#endif
ekmh = 0.d0
#ifdef LES
ekmhles = 0.d0
--- 185,194 ----
lout = .true.
loutfm = ioutfm <= 0
nr = nrp
#ifdef QMMM
nr = nr + nlink
#endif
+ nr3 = 3*nr
ekmh = 0.d0
#ifdef LES
ekmhles = 0.d0
***************
*** 206,212 ****
end if
#else
istart = 1
! iend = natom
#endif
istart3 = 3*istart -2
iend3 = 3*iend
--- 206,212 ----
end if
#else
istart = 1
! iend = nr
#endif
istart3 = 3*istart -2
iend3 = 3*iend
***************
*** 425,430 ****
--- 425,436 ----
fiti = 0.d0
fit2 = 0.d0
+ #ifdef QMMM
+ ! Set ntnb=1 to ensure that we always do an initial non-bond list update
+ ! before doing any MD, even if this is a restart.
+ ntnb = 1
+ #endif
+
do i = 1,nren
ener(i) = 0.0d0
enert(i) = 0.0d0
***************
*** 460,466 ****
! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
! MASS -----
! call ekcmr(nspm,nsp,tma,ekcmt,xr,v,amass,1,natom)
end if
! ----- CALCULATE THE FORCE -----
--- 466,472 ----
! ----- CALCULATE THE CENTER OF MASS ENERGY AND THE COORDINATES
! OF THE SUB-MOLECULES WITH RESPECT TO ITS OWN CENTER OF
! MASS -----
! call ekcmr(nspm,nsp,tma,ekcmt,xr,v,amass,1,nr)
end if
! ----- CALCULATE THE FORCE -----
***************
*** 477,483 ****
iprint = 1
! TIME_force is started and stopped inside force
#ifdef QMMM
- if(nstep == 0) ntnb = 1
call forcecp(xx,ix,ih,ipairs,x,f,ener(23),vir, &
r_stack, xx(l96), xx(l97), xx(l98), &
do_list_update, ifqnt, nquant, &
--- 483,488 ----
***************
*** 937,946 ****
nstep + 1
#ifdef PSANDER
endif
! call setvel(natom,v,winv,temp0*factt,init,iscale,scalm)
if (ibelly > 0) call bellyf(nr,ix(ibellygp),v)
#else
! call setvel(natom,v,winv,temp0*factt,init,iscale,scalm)
#ifdef LES
! newvel call is fixed for the dual target temperatures
--- 942,951 ----
nstep + 1
#ifdef PSANDER
endif
! call setvel(nr,v,winv,temp0*factt,init,iscale,scalm)
if (ibelly > 0) call bellyf(nr,ix(ibellygp),v)
#else
! call setvel(nr,v,winv,temp0*factt,init,iscale,scalm)
#ifdef LES
! newvel call is fixed for the dual target temperatures
***************
*** 1019,1025 ****
! in order. The unused results are thrown away
i3 = 3*(istart-1)
! do j=1,natom
if( jiend ) then
call gauss( 0.d0, 1.d0, fln )
call gauss( 0.d0, 1.d0, fln )
--- 1024,1030 ----
! in order. The unused results are thrown away
i3 = 3*(istart-1)
! do j=1,nr
if( jiend ) then
call gauss( 0.d0, 1.d0, fln )
call gauss( 0.d0, 1.d0, fln )
***************
*** 1567,1576 ****
! --- now compute the com motion, remove it, and recompute (just
! to check that it is really gone.....)
! call cenmas(natom,f,v,tmass,tmassinv,amass,ekcm, &
xcm,vcm,acm,ekrot,ocm,4)
! call stopcm(natom,f,v,xcm,vcm,ocm)
! call cenmas(natom,f,v,tmass,tmassinv,amass,ekcm, &
xcm,vcm,acm,ekrot,ocm,4)
else
--- 1572,1581 ----
! --- now compute the com motion, remove it, and recompute (just
! to check that it is really gone.....)
! call cenmas(nr,f,v,tmass,tmassinv,amass,ekcm, &
xcm,vcm,acm,ekrot,ocm,4)
! call stopcm(nr,f,v,xcm,vcm,ocm)
! call cenmas(nr,f,v,tmass,tmassinv,amass,ekcm, &
xcm,vcm,acm,ekrot,ocm,4)
else
***************
*** 1822,1828 ****
if (itdump) then
if( iwrap == 0 ) then
! call corpac(x,1,nrx,12,loutfm)
if(ntb > 0) call corpac(box,1,3,12,loutfm)
else
call get_stack(l_temp,3*natom)
--- 1827,1833 ----
if (itdump) then
if( iwrap == 0 ) then
! call corpac(x,1,3*natom,12,loutfm)
if(ntb > 0) call corpac(box,1,3,12,loutfm)
else
call get_stack(l_temp,3*natom)
***************
*** 1835,1841 ****
if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
end if
#endif
! call corpac(r_stack(l_temp),1,nrx,12,loutfm)
if(ntb > 0) call corpac(box,1,3,12,loutfm)
call free_stack(l_temp)
end if
--- 1840,1846 ----
if (ifbox == 2) call wrap_to(nspm,nsp,r_stack(l_temp),box)
end if
#endif
! call corpac(r_stack(l_temp),1,3*natom,12,loutfm)
if(ntb > 0) call corpac(box,1,3,12,loutfm)
call free_stack(l_temp)
end if
***************
*** 1844,1850 ****
! Velocity archive:
if (ntwv > 0) then
! if (mod(nstep,ntwv) == 0) call corpac(v,1,nrx,13,loutfm)
end if
! Energy archive:
--- 1849,1855 ----
! Velocity archive:
if (ntwv > 0) then
! if (mod(nstep,ntwv) == 0) call corpac(v,1,3*natom,13,loutfm)
end if
! Energy archive:
*** src/sander/sander.f 2004/05/03 17:49:03 7.206
--- src/sander/sander.f 2004/06/18 16:05:37
***************
*** 912,918 ****
klink = nlink
call link_atoms(nbona,x(Lcrd),nlink,npert,ix(iiba), &
ix(ijba),x(Lcrd+3*natom),nquant, &
! labels,natom,x(Lwinv+natom),mmqmbo(1),mmqmbo(2), &
ix(icnstrgp+nr))
if((imin.eq.0).and.(nlink.ne.0).and.(klink.eq.0)) then
write(6,*) 'FATAL ERROR'
--- 912,918 ----
klink = nlink
call link_atoms(nbona,x(Lcrd),nlink,npert,ix(iiba), &
ix(ijba),x(Lcrd+3*natom),nquant, &
! labels,natom,x(Lwinv+natom),x(Lmass+natom),mmqmbo(1),mmqmbo(2), &
ix(icnstrgp+nr))
if((imin.eq.0).and.(nlink.ne.0).and.(klink.eq.0)) then
write(6,*) 'FATAL ERROR'
***************
*** 926,943 ****
end if
if(nbona.gt.0) then
! itemp = nbona
! call del_bond2(nbona,ix(iibh+nbonh),ix(ijbh+nbonh), &
! ix(iicbh+nbonh),ix(iiba),ix(ijba),ix(iicba), &
nquant,labels)
- idiff = itemp - nbona
- nbona = nbona - idiff
-
- ! adjust memory location pointers to reflect changes in bonding
-
- Iiba = Iibh + nbonh
- Ijba = Ijbh + nbonh
- Iicba = Iicbh + nbonh
end if
! now that all of the "qm bonds" have been deleted from the bond lists
--- 926,933 ----
end if
if(nbona.gt.0) then
! call del_bond(nbona,ix(iiba),ix(ijba),ix(iicba), &
nquant,labels)
end if
! now that all of the "qm bonds" have been deleted from the bond lists
*** src/divcon/dcartcl.f 2004/01/15 00:31:12 1.1
--- src/divcon/dcartcl.f 2004/06/18 16:06:21
***************
*** 27,34 ****
IMPLICIT DOUBLE PRECISION (A-H,O-Z)
#include "divcon.dim"
#include "divcon.h"
!
! c#include "sizesqm.h"
DIMENSION COORD(3,*), DXYZQM(3,*),crdsmm(*),DXYZMM(3,*),
. chrgs(*),iqmres(*),mark(*),jqatms(*)
dimension xyz_qm(3),xyz_mm(3),psum(171)
--- 27,34 ----
IMPLICIT DOUBLE PRECISION (A-H,O-Z)
#include "divcon.dim"
#include "divcon.h"
! #include "sizesqm.h"
!
DIMENSION COORD(3,*), DXYZQM(3,*),crdsmm(*),DXYZMM(3,*),
. chrgs(*),iqmres(*),mark(*),jqatms(*)
dimension xyz_qm(3),xyz_mm(3),psum(171)
***************
*** 93,99 ****
c DEBUG = (INDEX(KEYWRD,'DCART') .NE. 0)
c FORCE = (INDEX(KEYWRD,'PREC')+INDEX(KEYWRD,'FORCE') .NE. 0)
ENDIF
! do 20 i=1,natoms
do 10 j=1,3
dxyzmm(j,i) = 0.0d0
10 continue
--- 93,99 ----
c DEBUG = (INDEX(KEYWRD,'DCART') .NE. 0)
c FORCE = (INDEX(KEYWRD,'PREC')+INDEX(KEYWRD,'FORCE') .NE. 0)
ENDIF
! do 20 i=1,mxatom
do 10 j=1,3
dxyzmm(j,i) = 0.0d0
10 continue
*** src/divcon/qm_mm.f 2004/01/15 00:31:23 1.1
--- src/divcon/qm_mm.f 2004/06/18 16:08:07
***************
*** 46,52 ****
#include "divcon.dim"
#include "divcon.h"
! c#include "OLD/SIZES"
C character keywrd*241
C
--- 46,52 ----
#include "divcon.dim"
#include "divcon.h"
! #include "sizesqm.h"
C character keywrd*241
C
***************
*** 66,73 ****
c COMMON /DIPSTO/ UX,UY,UZ,CH(NUMATM)
c#include "../sizesqm.h"
- parameter (mxatom=20000)
-
dimension qcords(3,mxatom),jqatms(*),mlabel(*),x(*),chrgs(*)
dimension qmlink(*),forces(*)
dimension dxyzqm(3,mxatom),dxyzcl(3,mxatom)
--- 66,71 ----
***************
*** 151,157 ****
$ nquatm,x,chrgs,iread,
$ iqmres,mark,jqatms)
endif
! call wrttims
if (icalcf.eq.0) then
call gcart(dxyzqm)
if (idc.eq.1) then
--- 149,155 ----
$ nquatm,x,chrgs,iread,
$ iqmres,mark,jqatms)
endif
! c call wrttims
if (icalcf.eq.0) then
call gcart(dxyzqm)
if (idc.eq.1) then
***************
*** 167,181 ****
call atmchg
call wrtchg
endif
! write(iout,'(/" ELECTRONIC ENERGY = ",f25.8," EV",
! . /" CORE-CORE REPULSIONS = ",f25.8," EV")')
! . eelect,ecore
! write(iout,'(" TOTAL ENERGY = ",f25.8," EV",
! . /" HEAT OF FORMATION = ",f25.8," KCAL/MOL")')
! . etot,escf
! write(iout,'(" FERMI ENERGY = ",f25.8," EV")')
! . efermi(1)
! call wrtxyz
c
c calculate electrostatic potential
c
--- 165,179 ----
call atmchg
call wrtchg
endif
! c write(iout,'(/" ELECTRONIC ENERGY = ",f25.8," EV",
! c . /" CORE-CORE REPULSIONS = ",f25.8," EV")')
! c . eelect,ecore
! c write(iout,'(" TOTAL ENERGY = ",f25.8," EV",
! c . /" HEAT OF FORMATION = ",f25.8," KCAL/MOL")')
! c . etot,escf
! c write(iout,'(" FERMI ENERGY = ",f25.8," EV")')
! c . efermi(1)
! c call wrtxyz
c
c calculate electrostatic potential
c
***************
*** 218,224 ****
enddo
endif
enddo
! else
do 300 i=1,nquatm
m = jqatms(i)
do 320 j=1,3
--- 216,227 ----
enddo
endif
enddo
! do i=1,ntotatm
! do j=1,3
! forces((i-1)*3+j) = forces((i-1)*3+j) - dxyzcl(j,i)
! enddo
! enddo
! else
do 300 i=1,nquatm
m = jqatms(i)
do 320 j=1,3
*** src/divcon/rotatecl.f 2004/01/15 00:31:30 1.1
--- src/divcon/rotatecl.f 2004/06/18 16:13:09
***************
*** 106,117 ****
write(iout,*) 'Program terminated'
stop
C
! ELSE IF (ITYPE.EQ.4) THEN
C
C MINDO CASE
C
! write(iout,*) 'MINDO not supported -- program terminated'
! stop
C
C MNDO, AM1 PM3 CASES
C
--- 106,117 ----
write(iout,*) 'Program terminated'
stop
C
! C ELSE IF (ITYPE.EQ.4) THEN
C
C MINDO CASE
C
! C write(iout,*) 'MINDO not supported -- program terminated'
! C stop
C
C MNDO, AM1 PM3 CASES
C
***************
*** 212,234 ****
SCALE = EXP(-ACI*RIJ)+EXP(-alph_mm*RIJ)
ENUC = ZNUCI*chrg_mm*GAM
SCALE=ABS(SCALE*ENUC)
! if(igauss.eq.1)then
! c
! c Add on gaussion functions for QM atom. This repulsion term
! c historically has not been used in QM/MM calculations.
! c
! C IF(ITYPE.EQ.2.OR.ITYPE.EQ.3)THEN
! DO 40 IG=1,4
! C IF(ABS(FN1(NI,IG)).GT.0.0D0)THEN
! AX = BGI(IG)*(RIJ-CGI(IG))**2
! IF(AX.LE.25.0D0)THEN
! SCALE = SCALE +
! . ZNUCI*chrg_mm/RIJ*AGI(IG)*EXP(-AX)
! ENDIF
! C ENDIF
! 40 CONTINUE
! C ENDIF
! endif
ENUC=ENUC+SCALE
ENDIF
RETURN
--- 212,234 ----
SCALE = EXP(-ACI*RIJ)+EXP(-alph_mm*RIJ)
ENUC = ZNUCI*chrg_mm*GAM
SCALE=ABS(SCALE*ENUC)
! C if(igauss.eq.1)then
! Cc
! Cc Add on gaussion functions for QM atom. This repulsion term
! Cc historically has not been used in QM/MM calculations.
! Cc
! CC IF(ITYPE.EQ.2.OR.ITYPE.EQ.3)THEN
! C DO 40 IG=1,4
! CC IF(ABS(FN1(NI,IG)).GT.0.0D0)THEN
! C AX = BGI(IG)*(RIJ-CGI(IG))**2
! C IF(AX.LE.25.0D0)THEN
! C SCALE = SCALE +
! C . ZNUCI*chrg_mm/RIJ*AGI(IG)*EXP(-AX)
! C ENDIF
! CC ENDIF
! C 40 CONTINUE
! CC ENDIF
! C endif
ENUC=ENUC+SCALE
ENDIF
RETURN
*** test/qmmm/standard/lysine.out.save 2004/03/11 23:23:47 1.6
--- test/qmmm/standard/lysine.out.save 2004/06/18 16:26:39
***************
*** 3,9 ****
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
! | Run on 01/26/2004 at 01:10:40
[-O]verwriting output
File Assignments:
--- 3,9 ----
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
! | Run on 06/18/2004 at 09:21:31
[-O]verwriting output
File Assignments:
***************
*** 28,34 ****
imin =1, maxcyc = 20, drms=0.005,
scee=1.2, ntpr=5, ntb=0, cut=99.,
ifqt=1, nqt= 3, idc=0
! /
8 9 10
END
END
--- 28,34 ----
imin =1, maxcyc = 20, drms=0.005,
scee=1.2, ntpr=5, ntb=0, cut=99.,
ifqt=1, nqt= 3, idc=0
! /
8 9 10
END
END
***************
*** 50,62 ****
| Memory Use Allocated
! | Real 4176
| Hollerith 1635
! | Integer 22805
| Max Pairs 231
| Max Rstack 50220
| Max Istack 110
! | Total 521 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--- 50,62 ----
| Memory Use Allocated
! | Real 5886
| Hollerith 1635
! | Integer 23449
| Max Pairs 231
| Max Rstack 50220
| Max Istack 110
! | Total 537 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
***************
*** 116,154 ****
NSTEP ENERGY RMS GMAX NAME NUMBER
! 5 1.1240E+00 1.2476E+01 4.8342E+01 C 21
! BOND = 0.3067 ANGLE = 0.4890 DIHED = 0.0039
! VDWAALS = 0.2595 EEL = -5.6916 HBOND = 0.0000
! 1-4 VDW = 3.6343 1-4 EEL = 61.6404 RESTRAINT = 0.0000
! ESCF = -59.5182
NSTEP ENERGY RMS GMAX NAME NUMBER
! 10 1.2645E+00 2.8947E+01 1.2481E+02 C 21
! BOND = 0.5395 ANGLE = 0.5698 DIHED = 0.0046
! VDWAALS = 0.2956 EEL = -5.6340 HBOND = 0.0000
! 1-4 VDW = 3.6447 1-4 EEL = 61.6286 RESTRAINT = 0.0000
! ESCF = -59.7843
NSTEP ENERGY RMS GMAX NAME NUMBER
! 15 1.2691E+00 4.6916E+01 2.0912E+02 C 21
! BOND = 0.5454 ANGLE = 0.5716 DIHED = 0.0046
! VDWAALS = 0.2965 EEL = -5.6328 HBOND = 0.0000
! 1-4 VDW = 3.6451 1-4 EEL = 61.6285 RESTRAINT = 0.0000
! ESCF = -59.7897
NSTEP ENERGY RMS GMAX NAME NUMBER
! 20 1.2681E+00 6.4973E+01 2.9359E+02 C 21
! BOND = 0.5441 ANGLE = 0.5712 DIHED = 0.0046
! VDWAALS = 0.2963 EEL = -5.6331 HBOND = 0.0000
! 1-4 VDW = 3.6450 1-4 EEL = 61.6285 RESTRAINT = 0.0000
! ESCF = -59.7886
Maximum number of minimization cycles reached.
--- 116,154 ----
NSTEP ENERGY RMS GMAX NAME NUMBER
! 5 7.3477E-01 2.4227E+00 7.9326E+00 N 1
! BOND = 0.0972 ANGLE = 0.4191 DIHED = 0.0039
! VDWAALS = 0.1497 EEL = -5.7891 HBOND = 0.0000
! 1-4 VDW = 3.4866 1-4 EEL = 61.5670 RESTRAINT = 0.0000
! ESCF = -59.1996
NSTEP ENERGY RMS GMAX NAME NUMBER
! 10 -2.1110E-01 9.5830E-01 4.1484E+00 CG 8
! BOND = 0.2291 ANGLE = 0.9455 DIHED = 0.0151
! VDWAALS = -0.0998 EEL = -5.6180 HBOND = 0.0000
! 1-4 VDW = 3.0296 1-4 EEL = 61.2042 RESTRAINT = 0.0000
! ESCF = -59.9167
NSTEP ENERGY RMS GMAX NAME NUMBER
! 15 -4.2612E-01 1.0603E+00 3.3223E+00 C 21
! BOND = 0.3464 ANGLE = 1.1014 DIHED = 0.0189
! VDWAALS = -0.1971 EEL = -5.5027 HBOND = 0.0000
! 1-4 VDW = 2.9251 1-4 EEL = 61.0328 RESTRAINT = 0.0000
! ESCF = -60.1508
NSTEP ENERGY RMS GMAX NAME NUMBER
! 20 -6.5331E-01 9.8858E-01 2.8940E+00 N 1
! BOND = 0.4478 ANGLE = 1.4345 DIHED = 0.0264
! VDWAALS = -0.3677 EEL = -5.2667 HBOND = 0.0000
! 1-4 VDW = 2.8055 1-4 EEL = 60.6462 RESTRAINT = 0.0000
! ESCF = -60.3792
Maximum number of minimization cycles reached.
***************
*** 159,190 ****
NSTEP ENERGY RMS GMAX NAME NUMBER
! 20 1.2681E+00 6.4973E+01 2.9359E+02 C 21
! BOND = 0.5441 ANGLE = 0.5712 DIHED = 0.0046
! VDWAALS = 0.2963 EEL = -5.6331 HBOND = 0.0000
! 1-4 VDW = 3.6450 1-4 EEL = 61.6285 RESTRAINT = 0.0000
! ESCF = -59.7886
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
! | Read coords time 0.00 ( 0.54% of Total)
! | Fast Water setup 0.00 ( 0.18% of Total)
! | Nonbond force 0.00 ( 9.96% of Force)
! | QMMM energy 0.04 (84.85% of Force)
! | Bond/Angle/Dihedral 0.00 ( 4.76% of Force)
! | Other 0.00 ( 0.43% of Force)
! | Force time 0.05 (100.0% of Runmd)
! | Runmd Time 0.05 (83.54% of Total)
! | Other 0.01 (15.73% of Total)
! | Total time 0.06 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
! | Job began at 01:10:40.034 on 01/26/2004
! | Setup done at 01:10:40.041 on 01/26/2004
! | Run done at 01:10:40.089 on 01/26/2004
! | wallclock() was called 530 times
--- 159,188 ----
NSTEP ENERGY RMS GMAX NAME NUMBER
! 20 -6.5331E-01 9.8858E-01 2.8940E+00 N 1
! BOND = 0.4478 ANGLE = 1.4345 DIHED = 0.0264
! VDWAALS = -0.3677 EEL = -5.2667 HBOND = 0.0000
! 1-4 VDW = 2.8055 1-4 EEL = 60.6462 RESTRAINT = 0.0000
! ESCF = -60.3792
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
! | Read coords time 0.02 ( 1.10% of Total)
! | Nonbond force 0.02 ( 2.08% of Force)
! | QMMM energy 0.93 (96.78% of Force)
! | Bond/Angle/Dihedral 0.01 ( 1.14% of Force)
! | Force time 0.96 (100.0% of Runmd)
! | Runmd Time 0.96 (52.77% of Total)
! | Other 0.84 (46.13% of Total)
! | Total time 1.82 (98.38% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
! | Job began at 09:21:30.963 on 06/18/2004
! | Setup done at 09:21:31.754 on 06/18/2004
! | Run done at 09:21:32.836 on 06/18/2004
! | wallclock() was called 588 times
*** test/qmmm/divcon/crambin.out.save 2004/03/11 23:23:47 1.6
--- test/qmmm/divcon/crambin.out.save 2004/06/18 16:29:20
***************
*** 3,9 ****
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
! | Run on 03/04/2004 at 01:21:35
[-O]verwriting output
File Assignments:
--- 3,9 ----
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
! | Run on 06/18/2004 at 09:27:33
[-O]verwriting output
File Assignments:
***************
*** 20,34 ****
|INPDIP: inpdip
|RSTDIP: rstdip
!
Here is the input file:
!
Crambin: 5 cycles minimization using D&C qm calculation
&cntrl
imin =1, maxcyc = 5, drms=0.005,
scee=1.2, ntpr=1, ntb=0, cut=8.1,
ifqt=1, nqt= 80, idc=1,
! /
80 81 82 83 84 85 86 87 88 89 90
91 92 99 100 101 102 103 104
105 106 107 108 115 116 117 118
--- 20,34 ----
|INPDIP: inpdip
|RSTDIP: rstdip
!
Here is the input file:
!
Crambin: 5 cycles minimization using D&C qm calculation
&cntrl
imin =1, maxcyc = 5, drms=0.005,
scee=1.2, ntpr=1, ntb=0, cut=8.1,
ifqt=1, nqt= 80, idc=1,
! /
80 81 82 83 84 85 86 87 88 89 90
91 92 99 100 101 102 103 104
105 106 107 108 115 116 117 118
***************
*** 60,72 ****
| Memory Use Allocated
! | Real 25280
| Hollerith 5400
| Integer 55343
| Max Pairs 205761
| Max Rstack 56420
| Max Istack 3210
! | Total 1691 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--- 60,72 ----
| Memory Use Allocated
! | Real 26010
| Hollerith 5400
| Integer 55343
| Max Pairs 205761
| Max Rstack 56420
| Max Istack 3210
! | Total 1697 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
***************
*** 117,164 ****
NSTEP ENERGY RMS GMAX NAME NUMBER
! 1 1.6067E+03 2.6375E+02 4.2280E+03 SG 373
! BOND = 51.8279 ANGLE = 71.9091 DIHED = 175.6588
VDWAALS = 2106.9976 EEL = -3217.8815 HBOND = 0.0000
1-4 VDW = 179.4333 1-4 EEL = 2334.7305 RESTRAINT = 0.0000
ESCF = -95.9452
NSTEP ENERGY RMS GMAX NAME NUMBER
! 2 1.5493E+03 2.5693E+02 4.1174E+03 SG 373
! BOND = 51.7529 ANGLE = 71.8969 DIHED = 175.6565
! VDWAALS = 2049.6784 EEL = -3217.8951 HBOND = 0.0000
! 1-4 VDW = 179.4366 1-4 EEL = 2334.7293 RESTRAINT = 0.0000
! ESCF = -96.0023
NSTEP ENERGY RMS GMAX NAME NUMBER
! 3 1.4822E+03 2.4899E+02 3.9889E+03 SG 373
! BOND = 51.6618 ANGLE = 71.8833 DIHED = 175.6537
! VDWAALS = 1982.8540 EEL = -3217.9113 HBOND = 0.0000
! 1-4 VDW = 179.4406 1-4 EEL = 2334.7276 RESTRAINT = 0.0000
! ESCF = -96.0725
NSTEP ENERGY RMS GMAX NAME NUMBER
! 4 1.4045E+03 2.3982E+02 3.8403E+03 SG 373
! BOND = 51.5509 ANGLE = 71.8685 DIHED = 175.6504
! VDWAALS = 1905.3900 EEL = -3217.9309 HBOND = 0.0000
! 1-4 VDW = 179.4452 1-4 EEL = 2334.7254 RESTRAINT = 0.0000
! ESCF = -96.1592
NSTEP ENERGY RMS GMAX NAME NUMBER
! 5 1.3151E+03 2.2929E+02 3.6700E+03 SG 227
! BOND = 51.4155 ANGLE = 71.8529 DIHED = 175.6464
! VDWAALS = 1816.2003 EEL = -3217.9544 HBOND = 0.0000
! 1-4 VDW = 179.4506 1-4 EEL = 2334.7224 RESTRAINT = 0.0000
! ESCF = -96.2667
Maximum number of minimization cycles reached.
--- 117,164 ----
NSTEP ENERGY RMS GMAX NAME NUMBER
! 1 1.6080E+03 2.6376E+02 4.2280E+03 SG 373
! BOND = 53.1269 ANGLE = 71.9091 DIHED = 175.6588
VDWAALS = 2106.9976 EEL = -3217.8815 HBOND = 0.0000
1-4 VDW = 179.4333 1-4 EEL = 2334.7305 RESTRAINT = 0.0000
ESCF = -95.9452
NSTEP ENERGY RMS GMAX NAME NUMBER
! 2 1.5506E+03 2.5693E+02 4.1175E+03 SG 373
! BOND = 53.0505 ANGLE = 71.8970 DIHED = 175.6564
! VDWAALS = 2049.6793 EEL = -3217.8943 HBOND = 0.0000
! 1-4 VDW = 179.4364 1-4 EEL = 2334.7296 RESTRAINT = 0.0000
! ESCF = -96.0046
NSTEP ENERGY RMS GMAX NAME NUMBER
! 3 1.4835E+03 2.4900E+02 3.9889E+03 SG 373
! BOND = 52.9577 ANGLE = 71.8836 DIHED = 175.6537
! VDWAALS = 1982.8559 EEL = -3217.9096 HBOND = 0.0000
! 1-4 VDW = 179.4401 1-4 EEL = 2334.7283 RESTRAINT = 0.0000
! ESCF = -96.0776
NSTEP ENERGY RMS GMAX NAME NUMBER
! 4 1.4058E+03 2.3983E+02 3.8404E+03 SG 373
! BOND = 52.8446 ANGLE = 71.8690 DIHED = 175.6503
! VDWAALS = 1905.3932 EEL = -3217.9279 HBOND = 0.0000
! 1-4 VDW = 179.4444 1-4 EEL = 2334.7265 RESTRAINT = 0.0000
! ESCF = -96.1677
NSTEP ENERGY RMS GMAX NAME NUMBER
! 5 1.3164E+03 2.2930E+02 3.6700E+03 SG 373
! BOND = 52.7065 ANGLE = 71.8537 DIHED = 175.6463
! VDWAALS = 1816.2049 EEL = -3217.9499 HBOND = 0.0000
! 1-4 VDW = 179.4495 1-4 EEL = 2334.7240 RESTRAINT = 0.0000
! ESCF = -96.2794
Maximum number of minimization cycles reached.
***************
*** 169,199 ****
NSTEP ENERGY RMS GMAX NAME NUMBER
! 5 1.3151E+03 2.2929E+02 3.6700E+03 SG 227
!
! BOND = 51.4155 ANGLE = 71.8529 DIHED = 175.6464
! VDWAALS = 1816.2003 EEL = -3217.9544 HBOND = 0.0000
! 1-4 VDW = 179.4506 1-4 EEL = 2334.7224 RESTRAINT = 0.0000
! ESCF = -96.2667
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
! | Read coords time 0.01 ( 0.07% of Total)
! | Nonbond force 0.04 ( 0.52% of Force)
! | QMMM energy 7.10 (99.33% of Force)
! | Bond/Angle/Dihedral 0.01 ( 0.14% of Force)
! | Other 0.00 ( 0.01% of Force)
! | Force time 7.15 (100.0% of Runmd)
! | Runmd Time 7.15 (98.50% of Total)
! | Other 0.10 ( 1.43% of Total)
! | Total time 7.26 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
! | Job began at 01:21:35.039 on 03/04/2004
! | Setup done at 01:21:35.112 on 03/04/2004
! | Run done at 01:21:42.298 on 03/04/2004
| wallclock() was called 206 times
--- 169,198 ----
NSTEP ENERGY RMS GMAX NAME NUMBER
! 5 1.3164E+03 2.2930E+02 3.6700E+03 SG 373
+ BOND = 52.7065 ANGLE = 71.8537 DIHED = 175.6463
+ VDWAALS = 1816.2049 EEL = -3217.9499 HBOND = 0.0000
+ 1-4 VDW = 179.4495 1-4 EEL = 2334.7240 RESTRAINT = 0.0000
+ ESCF = -96.2794
+
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
! | Read coords time 0.01 ( 0.08% of Total)
! | Nonbond force 0.10 ( 0.81% of Force)
! | QMMM energy 12.19 (99.11% of Force)
! | Bond/Angle/Dihedral 0.01 ( 0.08% of Force)
! | Force time 12.30 (100.0% of Runmd)
! | Runmd Time 12.30 (98.48% of Total)
! | Other 0.18 ( 1.44% of Total)
! | Total time 12.49 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
! | Job began at 09:27:33.845 on 06/18/2004
! | Setup done at 09:27:34.025 on 06/18/2004
! | Run done at 09:27:46.333 on 06/18/2004
| wallclock() was called 206 times
*** src/sander/Makefile 2004/03/16 00:20:27 8.1
--- src/sander/Makefile 2004/06/17 17:31:04 8.2
***************
*** 136,142 ****
threeb.o tripl.o nmrrad.o decnvh.o \
fastwt.o echoin.o parallel.o jnrg.o \
shake.o ene.QMMM.o mdwrit.QMMM.o minrit.QMMM.o \
! set.o setmm.o dynlib.o mdfil.o nmlsrc.o \
pcshift.o align.o \
rstack.o istack.o rfree.o rgroup.o \
random.o lsqfit.o amopen.o \
--- 136,142 ----
threeb.o tripl.o nmrrad.o decnvh.o \
fastwt.o echoin.o parallel.o jnrg.o \
shake.o ene.QMMM.o mdwrit.QMMM.o minrit.QMMM.o \
! set.o setmm.o dynlib.QMMM.o mdfil.o nmlsrc.o \
pcshift.o align.o \
rstack.o istack.o rfree.o rgroup.o \
random.o lsqfit.o amopen.o \
***************
*** 502,507 ****
--- 502,511 ----
$(FC) -c $(FFLAGS) -o $@ _sander.f
# --- routines for sander.QMMM:
+
+ dynlib.QMMM.o: dynlib.f
+ $(FPP) -DQMMM dynlib.f > _dynlib.f
+ $(FC) -c $(FFLAGS) -o $@ _dynlib.f
printe.QMMM.o: printe.f
$(FPP) -DQMMM printe.f > _printe.f
*** test/qmmm/divcon/crambin_md.out.save 2004-03-11 16:40:21.000000000 -0800
--- test/qmmm/divcon/crambin_md.out.save 2004-06-18 11:33:31.000000000 -0700
***************
*** 3,9 ****
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
! | Run on 03/02/2004 at 12:12:18
[-O]verwriting output
File Assignments:
--- 3,9 ----
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
! | Run on 06/18/2004 at 11:32:49
[-O]verwriting output
File Assignments:
***************
*** 28,34 ****
imin =0, nstlim=10,
scee=1.2, ntpr=1, ntb=0, cut=8.1,
ifqt=1, nqt= 80, idc=1,
! /
80 81 82 83 84 85 86 87 88 89 90
91 92 99 100 101 102 103 104
105 106 107 108 115 116 117 118
--- 28,34 ----
imin =0, nstlim=10,
scee=1.2, ntpr=1, ntb=0, cut=8.1,
ifqt=1, nqt= 80, idc=1,
! /
80 81 82 83 84 85 86 87 88 89 90
91 92 99 100 101 102 103 104
105 106 107 108 115 116 117 118
***************
*** 60,72 ****
| Memory Use Allocated
! | Real 17536
| Hollerith 5400
| Integer 55343
| Max Pairs 205761
| Max Rstack 56420
| Max Istack 3210
! | Total 1631 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--- 60,72 ----
| Memory Use Allocated
! | Real 18266
| Hollerith 5400
| Integer 55343
| Max Pairs 205761
| Max Rstack 56420
| Max Istack 3210
! | Total 1637 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
***************
*** 116,228 ****
NB-update: NPAIRS = 94449 HBPAIR = 0
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
! Etot = -866.9698 EKtot = 0.0000 EPtot = -866.9698
! BOND = 13.7445 ANGLE = 75.7358 DIHED = 173.5178
1-4 NB = 172.5680 1-4 EEL = 2309.5141 VDWAALS = -271.4044
EELEC = -3215.6062 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.00 PRESS = 0.0
! Etot = -866.9698 EKtot = 0.0000 EPtot = -866.9698
! BOND = 13.7445 ANGLE = 75.7358 DIHED = 173.5178
1-4 NB = 172.5680 1-4 EEL = 2309.5141 VDWAALS = -271.4044
EELEC = -3215.6062 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 1.67 PRESS = 0.0
! Etot = -867.1063 EKtot = 3.2241 EPtot = -870.3304
! BOND = 12.8867 ANGLE = 75.0051 DIHED = 173.4872
! 1-4 NB = 172.4190 1-4 EEL = 2309.3034 VDWAALS = -271.5678
! EELEC = -3215.7262 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 5.54 PRESS = 0.0
! Etot = -867.3391 EKtot = 10.6932 EPtot = -878.0323
! BOND = 11.1917 ANGLE = 73.0103 DIHED = 173.4018
! 1-4 NB = 171.9992 1-4 EEL = 2308.6660 VDWAALS = -272.0499
! EELEC = -3216.0256 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 9.45 PRESS = 0.0
! Etot = -867.4061 EKtot = 18.2594 EPtot = -885.6655
! BOND = 10.2671 ANGLE = 70.2827 DIHED = 173.2802
! 1-4 NB = 171.3814 1-4 EEL = 2307.5924 VDWAALS = -272.8338
! EELEC = -3216.3475 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 12.54 PRESS = 0.0
! Etot = -867.1638 EKtot = 24.2249 EPtot = -891.3887
! BOND = 10.6285 ANGLE = 67.5332 DIHED = 173.1507
! 1-4 NB = 170.6619 1-4 EEL = 2306.0835 VDWAALS = -273.9011
! EELEC = -3216.5023 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 15.52 PRESS = 0.0
! Etot = -866.9821 EKtot = 29.9780 EPtot = -896.9600
! BOND = 11.2789 ANGLE = 65.4617 DIHED = 173.0481
! 1-4 NB = 169.9327 1-4 EEL = 2304.1671 VDWAALS = -275.2252
! EELEC = -3216.3493 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 18.77 PRESS = 0.0
! Etot = -867.0259 EKtot = 36.2533 EPtot = -903.2792
! BOND = 11.0953 ANGLE = 64.5874 DIHED = 173.0105
! 1-4 NB = 169.2576 1-4 EEL = 2301.9111 VDWAALS = -276.7513
! EELEC = -3215.8623 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 21.30 PRESS = 0.0
! Etot = -867.0781 EKtot = 41.1380 EPtot = -908.2161
! BOND = 10.2332 ANGLE = 65.1362 DIHED = 173.0753
! 1-4 NB = 168.6568 1-4 EEL = 2299.4251 VDWAALS = -278.3904
! EELEC = -3215.1518 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 22.09 PRESS = 0.0
! Etot = -866.9373 EKtot = 42.6589 EPtot = -909.5962
! BOND = 9.8683 ANGLE = 66.9992 DIHED = 173.2749
! 1-4 NB = 168.1032 1-4 EEL = 2296.8495 VDWAALS = -280.0343
! EELEC = -3214.4341 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 21.48 PRESS = 0.0
! Etot = -866.6459 EKtot = 41.4931 EPtot = -908.1390
! BOND = 10.7214 ANGLE = 69.7649 DIHED = 173.6325
! 1-4 NB = 167.5306 1-4 EEL = 2294.3332 VDWAALS = -281.5833
! EELEC = -3213.9580 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 12.84 PRESS = 0.0
! Etot = -867.0655 EKtot = 24.7923 EPtot = -891.8577
! BOND = 11.1916 ANGLE = 69.3516 DIHED = 173.2879
! 1-4 NB = 170.2510 1-4 EEL = 2303.7845 VDWAALS = -275.3741
! EELEC = -3215.5963 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 7.93 PRESS = 0.0
! Etot = 0.2031 EKtot = 15.3140 EPtot = 15.2196
! BOND = 1.1606 ANGLE = 3.8933 DIHED = 0.2057
! 1-4 NB = 1.7383 1-4 EEL = 5.1670 VDWAALS = 3.4815
! EELEC = 0.8035 EHBOND = 0.0000 RESTRAINT = 0.0000
! |E(PBS) = 0.2608
------------------------------------------------------------------------------
--- 116,241 ----
NB-update: NPAIRS = 94449 HBPAIR = 0
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
! Etot = -856.0350 EKtot = 0.0000 EPtot = -856.0350
! BOND = 24.6793 ANGLE = 75.7358 DIHED = 173.5178
1-4 NB = 172.5680 1-4 EEL = 2309.5141 VDWAALS = -271.4044
EELEC = -3215.6062 EHBOND = 0.0000 RESTRAINT = 0.0000
+ ESCF = -125.0394
------------------------------------------------------------------------------
! NSTEP = 1 TIME(PS) = 0.001 TEMP(K) = 0.02 PRESS = 0.0
! Etot = -856.0018 EKtot = 0.0332 EPtot = -856.0350
! BOND = 24.6793 ANGLE = 75.7358 DIHED = 173.5178
1-4 NB = 172.5680 1-4 EEL = 2309.5141 VDWAALS = -271.4044
EELEC = -3215.6062 EHBOND = 0.0000 RESTRAINT = 0.0000
+ ESCF = -125.0394
------------------------------------------------------------------------------
! NSTEP = 2 TIME(PS) = 0.002 TEMP(K) = 2.11 PRESS = 0.0
! Etot = -856.2042 EKtot = 4.0775 EPtot = -860.2818
! BOND = 23.1250 ANGLE = 74.9422 DIHED = 173.4796
! 1-4 NB = 172.4272 1-4 EEL = 2309.3410 VDWAALS = -271.5589
! EELEC = -3215.6356 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -126.4023
------------------------------------------------------------------------------
! NSTEP = 3 TIME(PS) = 0.003 TEMP(K) = 7.08 PRESS = 0.0
! Etot = -856.6141 EKtot = 13.6684 EPtot = -870.2825
! BOND = 19.5732 ANGLE = 72.8004 DIHED = 173.3731
! 1-4 NB = 172.0315 1-4 EEL = 2308.8151 VDWAALS = -272.0158
! EELEC = -3215.6774 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -129.1827
------------------------------------------------------------------------------
! NSTEP = 4 TIME(PS) = 0.004 TEMP(K) = 12.38 PRESS = 0.0
! Etot = -856.7865 EKtot = 23.9086 EPtot = -880.6951
! BOND = 16.2311 ANGLE = 69.9499 DIHED = 173.2208
! 1-4 NB = 171.4524 1-4 EEL = 2307.9223 VDWAALS = -272.7610
! EELEC = -3215.6122 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -131.0984
------------------------------------------------------------------------------
! NSTEP = 5 TIME(PS) = 0.005 TEMP(K) = 16.71 PRESS = 0.0
! Etot = -856.6969 EKtot = 32.2717 EPtot = -888.9686
! BOND = 14.3432 ANGLE = 67.2341 DIHED = 173.0568
! 1-4 NB = 170.7833 1-4 EEL = 2306.6563 VDWAALS = -273.7785
! EELEC = -3215.3021 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -131.9616
------------------------------------------------------------------------------
! NSTEP = 6 TIME(PS) = 0.006 TEMP(K) = 20.45 PRESS = 0.0
! Etot = -856.6346 EKtot = 39.5051 EPtot = -896.1397
! BOND = 13.5235 ANGLE = 65.4564 DIHED = 172.9226
! 1-4 NB = 170.1118 1-4 EEL = 2305.0366 VDWAALS = -275.0414
! EELEC = -3214.6582 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -133.4909
------------------------------------------------------------------------------
! NSTEP = 7 TIME(PS) = 0.007 TEMP(K) = 23.82 PRESS = 0.0
! Etot = -856.7552 EKtot = 46.0168 EPtot = -902.7720
! BOND = 12.9629 ANGLE = 65.1670 DIHED = 172.8628
! 1-4 NB = 169.4956 1-4 EEL = 2303.1223 VDWAALS = -276.4925
! EELEC = -3213.6938 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -136.1965
------------------------------------------------------------------------------
! NSTEP = 8 TIME(PS) = 0.008 TEMP(K) = 25.85 PRESS = 0.0
! Etot = -856.8532 EKtot = 49.9354 EPtot = -906.7886
! BOND = 12.7530 ANGLE = 66.5323 DIHED = 172.9210
! 1-4 NB = 168.9480 1-4 EEL = 2301.0153 VDWAALS = -278.0396
! EELEC = -3212.5404 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -138.3781
------------------------------------------------------------------------------
! NSTEP = 9 TIME(PS) = 0.009 TEMP(K) = 25.73 PRESS = 0.0
! Etot = -856.7500 EKtot = 49.6986 EPtot = -906.4487
! BOND = 13.6697 ANGLE = 69.3071 DIHED = 173.1346
! 1-4 NB = 168.4346 1-4 EEL = 2298.8499 VDWAALS = -279.5746
! EELEC = -3211.4175 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -138.8523
------------------------------------------------------------------------------
! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 24.15 PRESS = 0.0
! Etot = -856.5124 EKtot = 46.6529 EPtot = -903.1653
! BOND = 15.8617 ANGLE = 72.9092 DIHED = 173.5310
! 1-4 NB = 167.8825 1-4 EEL = 2296.7703 VDWAALS = -281.0031
! EELEC = -3210.5663 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -138.5507
------------------------------------------------------------------------------
A V E R A G E S O V E R 10 S T E P S
! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 15.83 PRESS = 0.0
! Etot = -856.5809 EKtot = 30.5768 EPtot = -887.1577
! BOND = 16.6722 ANGLE = 70.0034 DIHED = 173.2020
! 1-4 NB = 170.4135 1-4 EEL = 2304.7043 VDWAALS = -275.1670
! EELEC = -3214.0710 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = -132.9153
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
! NSTEP = 10 TIME(PS) = 0.010 TEMP(K) = 9.38 PRESS = 0.0
! Etot = 0.2598 EKtot = 18.1254 EPtot = 18.3276
! BOND = 4.1048 ANGLE = 3.7120 DIHED = 0.2475
! 1-4 NB = 1.6104 1-4 EEL = 4.3490 VDWAALS = 3.2914
! EELEC = 1.8284 EHBOND = 0.0000 RESTRAINT = 0.0000
! ESCF = 4.8014
! |E(PBS) = 0.0346
------------------------------------------------------------------------------
***************
*** 230,248 ****
5. TIMINGS
--------------------------------------------------------------------------------
! | Read coords time 0.01 ( 0.05% of Total)
! | Nonbond force 0.15 ( 0.69% of Force)
! | QMMM energy 21.54 (99.22% of Force)
! | Bond/Angle/Dihedral 0.02 ( 0.09% of Force)
! | Force time 21.71 (100.0% of Runmd)
! | Verlet update time 0.01 ( 0.05% of Runmd)
! | Runmd Time 21.72 (99.45% of Total)
! | Other 0.11 ( 0.51% of Total)
! | Total time 21.84 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
! | Job began at 12:12:18.246 on 03/02/2004
! | Setup done at 12:12:18.367 on 03/02/2004
! | Run done at 12:12:40.088 on 03/02/2004
| wallclock() was called 434 times
--- 243,262 ----
5. TIMINGS
--------------------------------------------------------------------------------
! | Read coords time 0.01 ( 0.02% of Total)
! | Nonbond force 0.11 ( 0.26% of Force)
! | QMMM energy 41.20 (99.68% of Force)
! | Bond/Angle/Dihedral 0.02 ( 0.06% of Force)
! | Force time 41.33 (99.59% of Runmd)
! | Verlet update time 0.16 ( 0.39% of Runmd)
! | Other 0.01 ( 0.03% of Runmd)
! | Runmd Time 41.50 (99.86% of Total)
! | Other 0.05 ( 0.12% of Total)
! | Total time 41.56 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
! | Job began at 11:32:49.556 on 06/18/2004
! | Setup done at 11:32:49.616 on 06/18/2004
! | Run done at 11:33:31.120 on 06/18/2004
| wallclock() was called 434 times
------------------------------------------------------------------------------
Temporary workarounds: none