Dear Amber users,
I would be most thankful for any help with regards to the following problem:
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.
In addition, adding the command: "image familiar center" does not help !.
Furthermore, When changing the number of snapshots the problem persist
though, it appears earlier or later depending on the number of snapshots
taken. Namely, it reappears in the same time frame of the visualized
trajectory.
I thank you in advance for your help.
Arik
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Received on Thu Aug 05 2010 - 17:30:04 PDT
