Many thanks, Justin. Problem solved.
> -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of Justin A. Lemkul > Sent: 07 December 2009 11:58 > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Strange Gromacs4 trajectory visualisation with VMD > > > > Kukol, Andreas wrote: > > 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 ? > > > > Have you tried using trjconv to correct for periodicity effects? The frames > of > trajectory files now contain "broken" molecules due to the implementation of > DD, > so molecules (at the very least) have to be made whole. Usually trjconv - > pbc > mol (or -pbc nojump) is the right way to start. > > -Justin -- 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
