[gmx-users] Strange Gromacs4 trajectory visualisation with VMD
a.kukol at herts.ac.uk
Mon Dec 7 13:51:15 CET 2009
Many thanks, Justin.
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> 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
> > 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
> trajectory files now contain "broken" molecules due to the implementation of
> so molecules (at the very least) have to be made whole. Usually trjconv -
> mol (or -pbc nojump) is the right way to start.
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