[gmx-users] PBS Script - trjconv Options

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 17 12:49:08 CEST 2008

> Hello,
> Simple question.  I am running constraint pulling and getting the .xtc 
> and .tpr output files in order to create a pdb video using trjconv.  I 
> am running simulations on a cluster, and so a pbs script must be 
> submitted with the necessary commands.  When using trjconv command, the 
> group must subsequently be specified.  Is there any way to modify the 
> below command to also select a specific group (i.e. - 1 for 'Protein').  
> For example, when using mdrun, the -ff option can be used to specify 
> which forcefield to use.  Is there something similar to this with 
> regards to the group selection when using trjconv?  Thanks.

Something like this?



> trjconv -s peptide.tpr -f trajectory.xtc -o pullvideo.pdb
> ______________________________
> Venkatesh Hariharan
> Pennsylvania State University
> Schreyer Honors College
> Undergraduate - Bioengineering
> "You must be the change you wish to see in the world."
> --Mohandas Karamchand Gandhi
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list