From: Mare Libero (mareliber27_at_yahoo.com)
Date: Tue Jul 16 2013 - 22:02:58 CDT
have a 2fs time-step simulation that crashed after 14.2ns with the error message:
Constraint failure in RATTLE algorithm for atom 4944!
Constraint failure; simulation has become unstable.
simulation instability and the RATTLE algorithm error are extensively
documented on this mailing list.
my case, repeating the simulation at 1fs fixed the problem. I was
wondering if there is anything theoretically wrong in restarting the
simulation from the point it crashed with a shorter time-step. I
understand that continuing the same simulation with different time-steps will create a heterogeneous trajectory with
different time increments per frame. But I cannot think of anything theoretically wrong
in doing so. Am I missing
since I am now trying to compare trajectories collected with
different time-steps, is there a way to visualize trajectories in VMD
as a function of the time rater than frame number (I know this question
may be more appropriate for the VMD mailing list).
in advance for any input,
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