Re: [AMBER] AMBER simulation heating step

From: David A Case via AMBER <>
Date: Sun, 5 Feb 2023 12:04:45 -0500

On Sun, Feb 05, 2023, Prithviraj Nandigrami wrote:
>Dear De. Case,

Please send amber-related questions to the mail reflector,,
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 for information on how to
>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

AMBER mailing list
Received on Sun Feb 05 2023 - 09:30:03 PST
Custom Search