Re: [AMBER] vlimit exceeded issue

From: David A Case <>
Date: Tue, 13 Dec 2011 11:32:17 -0500

On Tue, Dec 13, 2011, Xiaozhou Li wrote:
> (the last lines in the output file)
> vlimit exceeded for step 3; vmax = 21.5763
> vlimit exceeded for step 4; vmax = 115.6802
> vlimit exceeded for step 5; vmax = 221.8382
> vlimit exceeded for step 6; vmax = 74.7778
> vlimit exceeded for step 7; vmax = 42.8791

This is quite odd: these are not terrible vlimit messages (although they
may indicate that something is wrong with your potential).
Ordinarily, such messages would not stop execution of the program.

I would look carefully at the output of the minimization that preceeded this
step. It will tell you which atom had the maximum force, and low the energy
got. Be sure that the potential energy at the first step of the MD matches
that from the end of the minimization step (set ntpr=1 and nstlim=10 in the MD
run). Also, visualize the structure after minimzation, especially around the
Mg and ATP, to see if anything has gone awry.

...good luck....dac

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Received on Tue Dec 13 2011 - 09:00:03 PST
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