-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 11/23/2010 04:48 PM, ms wrote: > Dear GROMACS users, > > I am trying to visualize a trajectory with hundreds of peptides which > come and go out and in the faces of the periodic box. Problem is, when > they cross the periodic boundary, the visualization software (I tried > both VMD and PyMol) create visual artefacts by visualizing nonsensically > long bonds crossing the box -which I understand, since the algorithms > seem to have no clear notion of PBC. > > Using -pbc nojump or similar, given my experience with identical systems > only containing less peptides, is not going to work (peptides are going > to be "broken").
So I think a trjconv with the option -pbc whole will give a trajectory that gives nice visualization of unbroken peptides /Flo > > Since all I want is some nice snasphot of the trajectory to show and not > analysis, I feel that a much easier solution would be to find a setting > in the visualization softwares that simply do not visualize bonds longer > than a threshold. However I can't find such a setting. Does one exist? > Does a "PBC mode" exist? What kind of solution do you propose? I googled > quite a bit but I couldn't find much. > > Thanks, > Massimo > - -- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart Phone: +49(0)711/685-6-3613 Fax: +49-(0)711/685-6-3658 EMail: domm...@icp.uni-stuttgart.de Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAkzr5sUACgkQLpNNBb9GiPmrWwCgpRJrZCmXb2Xs4FYKqCpLeTIE GD4AnRweb/jmjNoxmNktgxZDl/wSXN2T =LVaD -----END PGP SIGNATURE----- -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
