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

Shima Arasteh shima_arasteh2001 at yahoo.com
Fri Jun 15 18:41:43 CEST 2012

Sorry, what do you mean by trajectory A and B?


 From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, June 15, 2012 9:04 PM
Subject: Re: [gmx-users] protein near the edges of simulation box

On 6/15/12 12:19 PM, Shima Arasteh wrote:
>   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?

You have to load the output trajectory from trjconv into VMD, not the original.  If you visualize trajectory A, then manipulate it to produce trajectory B, then trajectory B is no use to you unless you actually use it.


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

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


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