[gmx-users] how to check the intermediate coordinated even when the simulation is running

Kavyashree M hmkvsri at gmail.com
Fri Nov 9 13:06:04 CET 2012

Hi ananya,

You can get the coordinates using trjconv:
trjconv -f <file.xtc> -s <file.tpr> -o <file.pdb> -b <initial time in ps>
-e <final time in ps>
this will give you pdb at the time you have mentioned.

For your first question- as far as I know you need to check whether
there is any periodic image violation using g_mindist. Other things
what you have to check depends on the parameter you want to see.

Probably others may give a better answer regarding this.


On Fri, Nov 9, 2012 at 5:04 PM, ananyachatterjee <
ananyachatterjee at iiserkol.ac.in> wrote:

> I am very new to this MD simulation, by reading the tutorials in the
> website I have run an simulation and it is running from last 5 day and I am
> not getting whether it is running properly or not. Could any one kindly
> tell me how to see whether the simulation is running or not and also how
> can I check the intermediate coordinated even when the simulation is
> running. Kindly help me.
> --
> Ananya Chatterjee,
> --
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