[gmx-users] Visualizing of a peptide in a water box - using trjconv
birgit.hischenhuber at meduniwien.ac.at
Tue Jun 1 16:24:18 CEST 2010
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
Therefore I tried two things:
trjconv -f a.trr -o b.xtc -s c.tpr -skip 10 -pbc mol -ur compact -center
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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