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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