[gmx-users] Catenation and Visualization

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Apr 22 05:35:26 CEST 2016

Hi Suniba,

For the first part, look up 'periodic boundary conditions' (my oh my, there
should be a keyboard shortcut for that term). For the second part, it seems
you have loaded two files, and you should see two objects in the right side
panel of Pymol. You can turn visualization off by clicking an object.

Hope it helps,

On Apr 22, 2016 04:56, "suniba" <sun.iba2 at gmail.com> wrote:

> Hello everyone
> I have completed two independent 100 ns simulations of two differnt
> proteins in water. One is monomer and the other is trimer. Both simulations
> were allowed to run for 50 ns intially, after visulation, trajectories were
> 'correct' and then extended the simulation to 100 ns. Now after completion
> and catenation, when i converted the .xtc into movie.pdb using trjconv, the
> molecule seems broken in all the frames and i am not able to view it in
> cartoon style. Moreover, when i load the .pdb file of monomer or trimer in
> Pymol, Always two files are getting uploaded. I dont know what is the other
> file but it remains 'static' when i play the movie. Is this visualization
> problem or i madd a mistake in catenation? Can someone plz give insight
> With Regards
> Sent from my iPhone
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