[gmx-users] translation

[priyanka srivastava]

Dear Justin,

Thanks a lot for replying back.

These are the two things that I have tried but still the peptide does not come at the center:

1. trjconv -f complete_production.xtc -s test.tpr -o test.pdb -center zero -b 22000
Select group for centering
Protein

Select group for output
System

2. trjconv -f complete_production.xtc -s test.tpr -center zero -fit translation -b 22000 -o check2.pdb

Select group for translational fit
Selected 0: 'System'

Select group for centering
Selected 1: 'Protein'

Select group for output
System

I am using 3.3.3.

thnx,
Priyanka..



----- Original Message ----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, 12 August, 2008 12:05:26 AM
Subject: Re: [gmx-users] translation



priyanka srivastava wrote:
> Dear All,
> 
> I really apologize for asking a peptide translation related question 
> again. I have a lipid-peptide system and I have already carried out the 
> production run for 20ns. The peptide has moved towards one of the edges 
> (I didnt specify comm-grps in the mdp file). I have to translate the 
> peptide in the center of the bilayer. While using trjconv it translates 
> the peptide at 0,0,0 but shifts the lipid and water molecules as well 
> such that eventually the peptide lies near the edge only!

Without seeing what command you've actually tried, it's hard to make any 
recommendation.

> Is there any other tool which I should be using?

trjconv is the tool you want, it's just a matter of finding the right options. 
Under GMX 3.3.3, there is a -center flag that allows you to select a group for 
centering.  In my protein/membrane systems, it has always worked well (choose 
Protein for the group to be centered).

-Justin

> Kindly suggest me something,
> Priyanka.
> 
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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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