[gmx-users] charmm and oplsaa simulation results don't match

[sarbani chattopadhyay]

Hi everybody,
                    I had run a long 100ns simulation on a tripeptide using opls/aa force field and 
spc water model.
I got a few microstates.
Then I tried to run simulation on the same system using charmm force field and tip3p water 
model.
However I couldn't find the microstates. Within the first 10 ns the system adopts the final
 configuration that was observed in the simulation using oplsaa force field.
 
 
 The process I used to run gromacs with charmm and tip3p water model is
 
 pdb2gmx -f opls.gro -ff charmm -ter -water tip3p
 
 charmm27-run-addtop-gromacs-dihe.sh topol.top new.top
  
  
 mv new.top topol.top
 
 
 #### I did modify the top file to include "tip3p-charmm.itp" 
 for water topology.
 
 
 editconf -f conf.gro -o box.gro -bt cubic -d 0.75
 
 genbox -cs spc216.gro -cp box.gro -p topol.top -o solvated.gro
 
 grompp -zero -f em.mdp -c solvated.gro -o em.tpr
 
 
 mdrun -v -s em.tpr
 
 
 Then I generated the "tpr" file for 100ns.
 
 The em.mdp file includes :
 
 
 
;       User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
cpp                 = /usr/bin/cpp
constraints         =  none
integrator          =  steep
nsteps              =  100
;
;       Energy minimizing stuff
;
emtol               =  2000
emstep              =  0.01



nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1.0
rvdw                =  1.0
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no


The 100ns.mdp file includes:


;
;       User spoel (236)
;       Wed Nov  3 17:12:44 1993
;       Input file
;
title               =  Yo
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  50000000 ; total 10000 ps.
nstcomm             =  1
nstxout             =  250
nstvout             =  1000
nstfout             =  0
nstlog              =  250
nstenergy           =  250
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
rcoulomb            =  1.0
rvdw                =  1.0
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  SOL
tau_t               =  0.1      0.1
ref_t               =  300      300
; Energy monitoring
energygrps          =  Protein  SOL
; Isotropic pressure coupling is now on
Pcoupl              =  berendsen
Pcoupltype          = isotropic
tau_p               =  0.5
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is off at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529


Can anyone suggest why am I not getting the microstates with "charmm " force field.
Is there anything more that I needed to do and I missed. I am sorry for such a lengthy query


Thanks in advance

Sarbani
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