[gmx-users] Membrane protein tutorial
pawan.chinari at gmail.com
Thu Apr 9 07:17:24 CEST 2009
Thanks for your reply.
I have used this .mdp file. Is there anything wrong in the mdp file which I
am using ?
To tell you in detail : First I have done energy minimization. Output of
this step (box_em.pdb) is used to create an index group for sol and cl- ions
using make_ndx. Then I am trying to run grompp using this particular .mdp
file before position restraint mdrun.
*pr.mdp file :*
title = protein in popc bilayer
cpp = /usr/bin/cpp
define = -DPOSRES -DPOSRES_LIPID
constraints = all-bonds
integrator = md
dt = 0.002
nsteps = 5000
nstcomm = 1
nstxout = 50
nstvout = 1000
nstfout = 0
nstlog = 10
nstenergy = 10
nstlist = 10
ns_type = grid
rlist = 1
coulombtype = PME
rcoulomb = 1
vdw-type = Cut-off
rvdw = 1
; Berendsen temperature coupling is on in two groups
tcoupl = berendsen
tc_grps = Protein POPC SOL_CL-
tau_t = 0.1 0.1 0.1
ref_t = 300 300 300
; Energy monitoring
energygrps = Protein POPC SOL_CL-
; Pressure coupling is on
Pcoupl = berendsen
tau_p = 2.0 2.0
compressibility = 4.5e-5 4.5e-5
ref_p = 1.0 1.0
Pcoupl_type = semiisotropic
; Generate velocites is on at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
On Thu, Apr 9, 2009 at 10:38 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> Pawan Kumar wrote:
>> Hello Mark Sir,
>> I have tried that way also.
>> The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p
>> topol.top -o box_pr.tpr
>> But this time i get an error like this "Atom 1 defined in multiple groups
>> (1 & 3). "
>> How to overcome this error ?
> You can't have the same atom in multiple groups used for the same purpose
> within mdrun (e.g. T-coupling or energy). I guess you've constructed your
> index file in a manner that is inconsistent with your use of it.
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