[gmx-users] Strange Gromacs4 trajectory visualisation with VMD

Kukol, Andreas a.kukol at herts.ac.uk
Mon Dec 7 12:48:10 CET 2009

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

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