----- Original Message ----- From: Birgit Hischenhuber <birgit.hischenhu...@meduniwien.ac.at> Date: Wednesday, June 2, 2010 0:44 Subject: [gmx-users] Visualizing of a peptide in a water box - using trjconv To: gmx-users@gromacs.org
<!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; margin-bottom:.0001pt; font-size:12.0pt; font-family:"Times New Roman";} a:link, span.MsoHyperlink {color:blue; text-decoration:underline;} a:visited, span.MsoHyperlinkFollowed {color:purple; text-decoration:underline;} span.E-MailFormatvorlage17 {mso-style-type:personal-compose; font-family:Arial; color:windowtext;} @page Section1 {size:595.3pt 841.9pt; margin:70.85pt 70.85pt 2.0cm 70.85pt;} div.Section1 {page:Section1;} --> ----------------------------------------------------------- | > 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 I don't think -ur or -fit are useful for your problem. I suspect something like trjconv -center trjconv -pbc mol is what you want, perhaps even in one pass. Obviously, check trjconv -h for info - it suggests the combination of the above... Mark > 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
-- 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