[gmx-users] Strange Gromacs4 trajectory visualisation with VMD

Matthew Hoopes mihoopes at ucdavis.edu
Fri Dec 11 23:59:36 CET 2009

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.


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
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

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

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