On 8/5/2010 5:15 PM, arikcohen wrote:
> 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 Fri Aug 06 2010 - 17:00:04 PDT
