[gmx-users] Visualizing of a peptide in a water box - using trjconv

Mark Abraham mark.abraham at anu.edu.au
Tue Jun 1 20:41:31 CEST 2010

----- Original Message -----
From: Birgit Hischenhuber <birgit.hischenhuber at meduniwien.ac.at>
Date: Wednesday, June 2, 2010 0:44
Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv
To: gmx-users at gromacs.org

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  > Hi,
  > I simulate a peptide in a water box with some ions to get a neutral solution. I want to visualize the peptide in the water box.
  > I want that the peptide is in the center of the box, but also have a look at the water.
  > Therefore I tried two things:
  > trjconv –f a.trr –o b.xtc –s c.tpr –skip 10 –pbc mol –ur compact –center –fit progressive
  > Visualizing it with VMD I see the peptide centering in the middle of the box, but the water get during the time holes.
  > So I checked the mailing list and find some inputs and tried it with two steps:
  > trjconv –f a.trr –o b.xtc –s c.tpr –pbc mol –ur compact
  > trjconv –f b.xtc –o d.xtc –s c.tpr –skip 10 –center –fit progressive

I don't think -ur or -fit are useful for your problem. I suspect something like 

trjconv -center

trjconv -pbc mol

is what you want, perhaps even in one pass. Obviously, check trjconv -h for info - it suggests the combination of the above...


  > at this try I get a peptide in the center of the box and during the time the pepide moves to the edge of the box and I consider that the box rotate around the peptide.
  > Is there a possibility that my peptide stays in the center of the box and the water doesn’t get any holes?
  > Thanks a lot for your helps!
  > ---
  > DI Birgit Hischenhuber
  > Unit for Medical Statistics and Informatics 
  > Section for Biomedical Computersimulation and Bioinformatics
   > -- 
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