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<body class='hmmessage'><div style="text-align: left;"><br></div><br><br><br><hr id="EC_stopSpelling">From: gmx3@hotmail.com<br>To: sarbani_c84@rediffmail.com<br>Subject: RE: [gmx-users] charmm and oplsaa simulation results don't match<br>Date: Tue, 19 Aug 2008 10:47:02 +0200<br><br>
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<div style="text-align: left;">Hi,<br><br>There are two main issues here.<br><br>One is sampling. I don't know what the correlations times in your systems are.<br>You say you obtain a few microstates. But does the system revisit the same<br>microstates over the 100 ns? If not, your simulations are certainly too short<br>to have full sampling and you can not expect that two simulations with the same<br>or different force fields produce the same sampling.<br><br>The second issue is the force field. Different force fields can favor different<br>configurations. This is especially true for backbone dihedrals. This will have<br>stronger effects on small peptides than on larger (less flexible) proteins.<br></div><br>And finally, it seems you are running with a plain Coulomb cut-off.<br>This will produce artefacts. You should use PME (or at least a reaction-field).<br><br>Berk<br><br><hr id="EC_EC_stopSpelling">Date: Tue, 19 Aug 2008 08:28:25 +0000<br>From: sarbani_c84@rediffmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] charmm and oplsaa simulation results don't match<br><br>
<br>
Hi everybody,<br>
I had run a long 100ns simulation on a tripeptide using opls/aa force field and <br>
spc water model.<br>
I got a few microstates.<br>
Then I tried to run simulation on the same system using charmm force field and tip3p water <br>
model.<br>
However I couldn't find the microstates. Within the first 10 ns the system adopts the final<br>
configuration that was observed in the simulation using oplsaa force field.<br>
<br>
<br>
The process I used to run gromacs with charmm and tip3p water model is<br>
<br>
pdb2gmx -f opls.gro -ff charmm -ter -water tip3p<br>
<br>
charmm27-run-addtop-gromacs-dihe.sh topol.top new.top<br>
<br>
<br>
mv new.top topol.top<br>
<br>
<br>
#### I did modify the top file to include "tip3p-charmm.itp" <br>
for water topology.<br>
<br>
<br>
editconf -f conf.gro -o box.gro -bt cubic -d 0.75<br>
<br>
genbox -cs spc216.gro -cp box.gro -p topol.top -o solvated.gro<br>
<br>
grompp -zero -f em.mdp -c solvated.gro -o em.tpr<br>
<br>
<br>
mdrun -v -s em.tpr<br>
<br>
<br>
Then I generated the "tpr" file for 100ns.<br>
<br>
The em.mdp file includes :<br>
<br>
<br>
<br>
; User spoel (236)<br>
; Wed Nov 3 17:12:44 1993<br>
; Input file<br>
;<br>
cpp = /usr/bin/cpp<br>
constraints = none<br>
integrator = steep<br>
nsteps = 100<br>
;<br>
; Energy minimizing stuff<br>
;<br>
emtol = 2000<br>
emstep = 0.01<br>
<br>
<br>
<br>
nstcomm = 1<br>
ns_type = grid<br>
rlist = 1<br>
rcoulomb = 1.0<br>
rvdw = 1.0<br>
Tcoupl = no<br>
Pcoupl = no<br>
gen_vel = no<br>
<br>
<br>
The 100ns.mdp file includes:<br>
<br>
<br>
;<br>
; User spoel (236)<br>
; Wed Nov 3 17:12:44 1993<br>
; Input file<br>
;<br>
title = Yo<br>
cpp = /usr/bin/cpp<br>
constraints = all-bonds<br>
integrator = md<br>
dt = 0.002 ; ps !<br>
nsteps = 50000000 ; total 10000 ps.<br>
nstcomm = 1<br>
nstxout = 250<br>
nstvout = 1000<br>
nstfout = 0<br>
nstlog = 250<br>
nstenergy = 250<br>
nstlist = 10<br>
ns_type = grid<br>
rlist = 1.0<br>
rcoulomb = 1.0<br>
rvdw = 1.0<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tc-grps = Protein SOL<br>
tau_t = 0.1 0.1<br>
ref_t = 300 300<br>
; Energy monitoring<br>
energygrps = Protein SOL<br>
; Isotropic pressure coupling is now on<br>
Pcoupl = berendsen<br>
Pcoupltype = isotropic<br>
tau_p = 0.5<br>
compressibility = 4.5e-5<br>
ref_p = 1.0<br>
; Generate velocites is off at 300 K.<br>
gen_vel = no<br>
gen_temp = 300.0<br>
gen_seed = 173529<br>
<br>
<br>
Can anyone suggest why am I not getting the microstates with "charmm " force field.<br>
Is there anything more that I needed to do and I missed. I am sorry for such a lengthy query<br>
<br>
<br>
Thanks in advance<br>
<br>
Sarbani<br>
<br>
<br><br>
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