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

Kukol, Andreas a.kukol at herts.ac.uk
Tue Jun 1 16:48:48 CEST 2010

I don't think there is that possiblity, because protein diffusion is a natural process that occurs in your simulation.



From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Birgit Hischenhuber
Sent: 01 June 2010 15:24
To: gmx-users at gromacs.org
Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv


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

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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