[gmx-users] Catenation and Visualization

[Sun Iba]

Hello Tsjerk
Thank you for your response. I have applied periodic boundary conditions
and have loaded only one file i.e. movie.pdb in Pymol. Thats correct I can
turn visualization off but my question is why two objects are showing up
when I have catenated two trajectories. That's I asked if  used wrong
command for catenation or something is missing. See, I used:

gmx trjcat -f last.xtc latest.xtc -o 100ns.xtc

On Fri, Apr 22, 2016 at 9:05 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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,
>
> Tsjerk
> 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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