[gmx-users] problem with nvt equilibration

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 6 12:47:25 CET 2012

Anushree Tripathi wrote:
> where should I use -n option in the command (i.e., grompp -f nvt.mdp -c 
> em.gro -p topol.top -o nvt.tpr).Please tell me.

I would suggest you refer to grompp -h and/or go through some basic tutorial 
material so that you can get a feel for command line options and how to apply them.


> On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     On 6/02/2012 8:28 PM, Anushree Tripathi wrote:
>         Inspite of having DPPC in index file,when I run the command (
>         i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am
>         getting the error:
>         Group DPPC not found in indexfile.
>         Maybe you have non-default goups in your .mdp file, while not
>         using the '-n' option of grompp.
>         In that case use the '-n' option.
>         Now, what to do? Please guide me.
>     You seem not to have used the -n option. You could try using it. :)
>     Mark
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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