[gmx-users] Membrane protein tutorial

[Pawan Kumar]

Hello sir,

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
constraint-algorithm=  Lincs
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

Thanking you,
Pawan

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.
>
>
> Mark
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