I don't think there is that possiblity, because protein diffusion is a natural process that occurs in your simulation.
Andreas ----------------------- From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Birgit Hischenhuber Sent: 01 June 2010 15:24 To: gmx-users@gromacs.org Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv 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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
