[gmx-users] Strange Gromacs4 trajectory visualisation with VMD

[Kukol, Andreas]

Many thanks, Justin.
Problem solved.


> -----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
> 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