AW: [gmx-users] Visualizing of a peptide in a water box - usingtrjconv

Birgit Hischenhuber birgit.hischenhuber at
Tue Jun 1 16:57:26 CEST 2010

Aha, ok. Thank you!
And do you consider that the first or the second visualizing is better for

Regards, Birgit

-----Ursprüngliche Nachricht-----
Von: gmx-users-bounces at [mailto:gmx-users-bounces at] Im
Auftrag von Kukol, Andreas
Gesendet: Dienstag, 1. Juni 2010 16:49
An: Discussion list for GROMACS users
Betreff: RE: [gmx-users] Visualizing of a peptide in a water box -

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 [mailto:gmx-users-bounces at]
On Behalf Of Birgit Hischenhuber
Sent: 01 June 2010 15:24
To: gmx-users at
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

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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