[gmx-users] PBS Script - trjconv Options

VENKATESH HARIHARAN vuh105 at psu.edu
Tue Sep 16 22:38:03 CEST 2008


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.

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

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