[gmx-users] how to check the intermediate coordinated even when the simulation is running
hmkvsri at gmail.com
Fri Nov 9 13:06:04 CET 2012
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,
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
More information about the gromacs.org_gmx-users