[gmx-users] peptide translation

priyanka srivastava priyankaps4 at yahoo.com
Wed Aug 6 21:31:25 CEST 2008

Dear All,

I have a lipid - peptide system and while running the production run I forgot to assign comm-grps, thus the peptide has actually shifted from the center towards one of the edges. I have searched the forum and tried all possible options in trjconv i.e. -center zero, -fit translation, progressive etc. but mostly the entire bilayer shifts but the peptide does not move from its place. I am selecting the "Protein" option from trjconv when it asks for "group used for centering"
How to translate the peptide only in a lipid-peptide system to a certain point? This is a short peptide in the top layer of the lipid bilayer and my bilayer center is at (0,0,0). I want to put the peptide at (0,0,1.7). I even tried using the shift option, but that does some weird things.
Searching forum results in centering peptide in a water box i.e. peptide or protein at 0,0,0 and also mainly the threads that are already there talks about using trjconv center and translation options! I really apologize if I missed out any thread related to this and shall be really grateful if experts out there would kindly help me out.

eagerly waiting for the response,

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