[gmx-users] Visualization Problem

[Itamar Kass]

Shalom George

Maybe your nanotube 'jump' over the PBC?

Try 'trjconv -pbc whole ...'

Best,
Itamar

George Abadir wrote:
> Hi,
>     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,
> Regards,
> George
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-- 
"Prediction is very difficult, especially about the future" - Niels Bohr

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
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| Molecular Dynamics Group
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