[gmx-users] PBS Script - trjconv Options

[Justin A. Lemkul]

VENKATESH HARIHARAN wrote:
> 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?

http://wiki.gromacs.org/index.php/Making_Commands_Non-Interactive

-Justin

> 
> 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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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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