[gmx-users] Strange Gromacs4 trajectory visualisation with VMD

Justin A. Lemkul jalemkul at vt.edu
Mon Dec 7 12:57:41 CET 2009

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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