[gmx-users] Visualization Problem
ikass at uq.edu.au
Tue May 8 05:04:19 CEST 2007
Maybe your nanotube 'jump' over the PBC?
Try 'trjconv -pbc whole ...'
George Abadir wrote:
> I finished a simulation of a carbon nanotube in water. I made a
> movie of the simulation using 'trjconv' to view with Pymol. The problem
> is that starting from the third frame it messes the carbon nanotube
> bonds. I changed the start time and again in the third frames it messed
> things up. I output each frame in a different file using the '-sep'
> option and it could read each one successfuly, so I think the problem is
> in reading them in sequence. Can anyone help with that?
> Thank you very much,
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