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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