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 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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