[gmx-users] translation

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 11 20:35:26 CEST 2008

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 

> 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).


> 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


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