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,
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:23:28 CST