[gmx-users] Visualization Problem
georgea at ece.ubc.ca
Tue May 8 05:13:11 CEST 2007
Thanks Itamar for your reply, but the tube actually does not jump, but
the lines showing the bonds start to show bonding between
non-neighbouring atoms, i.e., the hexagonal shape characteristic of
nanotubes is destroyed, and it starts from the third frame regardless of
the start time. I tried the 'pbc whole' option anyway but it didn't work.
Thank you very much,
Itamar Kass wrote:
> Shalom George
> 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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