[gmx-users] Visualization Problem

George Abadir 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 ...'
> 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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