Re: AMBER: more vlimit exceeded problems...

From: David A. Case <>
Date: Wed, 7 Apr 2004 08:06:31 -0700

On Tue, Apr 06, 2004, Linda Prengaman wrote:

> I am running thermodynamic integration for a small system solvated in
> water. I am running the calculations concurrently for 5 clambda values.
> The runs for the first 3 lambdas were fine, but the 4th and 5th lambda runs
> returned a "vlimit exceeded" error after just a few steps and "nan" values
> for numbers. I am using an exact copy of my sander input file for all of
> the other lambda values, except with of course the lambda value changed,
> so I don't understand why my system is not working for this value. I have
> performed minimization and gotten a good value for energy and the other MD
> calculations I have done for this system were also stable. I have fixed
> my problem by changing my dt parameter from 1 fs to 0.5 fs, but I know
> this is not a practical fix because it doubles the time of my runs from 3
> hours to 6 or 7. Please email me if anyone out there has abetter solution
> to this problem.

I'm not sure that this problem can be figured out from just a qualitative
description, but a few questions might help. What sort of change are you
making to the system? Are dummy atoms being created? If so, you may need to
look at the klambda parameter. Are you using any non-standard force field

It is mostly likely that you have some sort of instability in your system that
is just being "found" by the trajectories you run. Since the error happens on
the first few steps, be sure to run a short calculation with ntpr=1; you may
see something that helps. Also, try the simulation that fails with various
values of clambda: it may be the starting coordinates and not the value of
lambda that is key here. You could use the "checkoverlap" command in ptraj
to see if there are any bad contacts in the starting coordinates of the run
that fails.

If these tests don't help, you will probably have to post your files to see
if someone else can try to reproduce the problem.

....hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Wed Apr 07 2004 - 16:53:00 PDT
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