[gmx-users] Trajectory visualization and PBC

Monique Brito moniquebrito at yahoo.com.br
Mon Aug 8 21:13:46 CEST 2005

> Hi, people,
> We're doing our simulation of a 953 residue
> protein in vacuo. 
> After energy minimization we run 3 ns of
> dynamics.
> When we visualize the trajectory without
> removing PBC, we
> don't see anything abnormal, but when we remove
> PBC, with trjconv, the structure shows a
> deformed and strange
> trajectory, with several strechted bonds, as if
> some chais were entirely moved 
> away from the rest of the body of the protein.
> But the plot of the potential energy vs.
> trajectory shows nothing wrong.
> Is it necessary to remove PBC to see the real
> trajectory or can we see it with PBC? Is it the
> same result?
> Thanks,
> Monique Brito

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