A quick and dirty fix that may save time is to view the trajectory in VMD with the DynamicsBonds drawing method instead of Lines (Graphics -> Representation -> Drawing Method -> DynamicBonds). This make bond lines based on distance. Otherwise use the -pdb flag with "whole" or similar choice with trjconv.
-Matt -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Kukol, Andreas Sent: Monday, December 07, 2009 3:48 AM To: Discussion list for GROMACS users Subject: [gmx-users] Strange Gromacs4 trajectory visualisation with VMD Hi all, When I look at the trajectory of a lipid/protein/water system generated with Gromacs 4.05 on four cores, the lipid bilayer looks messed up with bonds drawn all over the system, while the protein and water are displayed correctly. This is similar to previous Gromacs3 trajectories that had been shuffled, but not deshuffled before visualisation. Did anyone see similar problems and is there a solution to display the lipid correctly ? Many thanks Andreas -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
