[gmx-users] protein near the edges of simulation box

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 15 18:19:36 CEST 2012

 OK, but as I know the trjconv is a command after mdrun, so when I get the output of mdrun and see it in VMD, it doesn't make different. 
Now wondering what is the benefit of trjconv -center and -pbc?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, June 15, 2012 8:24 PM
Subject: Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 11:46 AM, Shima Arasteh wrote:
> Dear Elton,
> Where am I supposed to use trjconv -center ? when I want to get the mdrun?

trjconv is a post-processing command that can be used for a variety of purposes, of which one of the more common ones is to transform coordinates for convenient visualization through operations involving -center or -pbc.


-- ========================================

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120615/11147468/attachment.html>

More information about the gromacs.org_gmx-users mailing list