> When visualizing an equilibration trajectory (for 2ns, with 10000
> snapshots, taken every 100 steps, each step is 2fs), the trajectory is
> well behaving though after a while it collapses to a small ball like,
> appearing in different places every couple of steps(like in different
> unit cells). This problem seems to be a post-processing error as the
> potential and kinetic energy a long the trajectory seems just fine. i.e
> as they should be with no abnormal fluctuations.
> It should be mentioned, that this problem appears in both occasions when
> processing the mdcrd file to a truncated mdcrd or a truncated binpos
> file using ptraj.
Can you show your ptraj script? Can you view the whole trajectory
if it isn't massaged by ptraj? If you are stripping any atoms, are
you sure you are using a correct prmtop? Is it all from a single mdcrd?
What program are you using to visualize?
Bill
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Received on Fri Aug 06 2010 - 17:00:05 PDT
