On Sun, Feb 05, 2023, Prithviraj Nandigrami wrote:
>Dear De. Case,
Please send amber-related questions to the mail reflector, amber.ambermd.org,
and not to me personally. That way, many people can see your question and try
to help, and the answers can help others with similar questions. See
http://lists.ambermd.org/mailman/listinfo/amber for information on how to
subscribe.
>
>Thank you for your reply. So, I ran the simulations (minimization, heating,
>equilibration) using the CPU code (pmemd). It looks like the first two
>stages (minimization and heating) runs fine but then I ran into another
>issue during the equilibration step:
>
> t = 0.00000, dt = 0.00200, vlimit = 20.00000
>vlimit exceeded for step 55129; vmax = 51.4881
>vlimit exceeded for step 55130; vmax = 27.0144
OK: re-run this step with nstlim=55200, so you go just past the point where
vlimit problems occur. Visualize the trajectory near that point, and
use the "checkstructure" action in cpptraj to look for problems that might
be causing large forces. You are going to need to dig into the origin of
the vlimit problems.
...good luck....dac
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Received on Sun Feb 05 2023 - 09:30:03 PST
