[gmx-users] problem with nvt equilibration

[Mark Abraham]

On 6/02/2012 11:09 PM, Anushree Tripathi wrote:
> Will you please send me the basic tutorial in which I can find how to 
> use -n option in " grompp -f nvt.mdp -c em.gro -p topol.top -o 
> nvt.tpr" command.

All the tutorials provide examples of using the general syntax

command -x value -y file.ext

for various values of command, x, value, y and file.ext. These allow you 
to provide the command with the input to work on and the instructions 
for how to act. The option (x and y) provides a label for the values, so 
that you and the command both know what is input, or output, etc. 
command -h provides a list of all the options, and indicates the kind of 
data they might wish to have supplied with them.

You seem to be trying to do a membrane simulation. Likely any membrane 
simulation will have to deal with the issue of temperature coupling and 
the lipid group. You should complete any such tutorials you can find and 
understand them fully.

Mark

>
> On Mon, Feb 6, 2012 at 5:17 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     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.
>
>     -Justin
>
>         On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham
>         <Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>         <mailto: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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>
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