AMBER Archive (2005)

Subject: RE: AMBER: Error: vlimit exceeded for step

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 06 2005 - 22:49:05 CDT


Dear Hwankyu,

> "IFCAP=0".

My apologies, for some reason I thought you were running a stochastic
boundary simulation.

The water leaving into what looks like vacuum is not actually a problem in
periodic boundary simulations since it is re-imaged back into the central
box. You can re-image waters using ptraj so it looks better when you
visualise the trajectory.

However, you don't say how fast the waters are leaving, typically they
should diffuse out slowly. If, however, they are flying off at high speed
then you have something seriously wrong with the early stages of your
simulation. It just takes a while to fail.

This is about the best I can do I'm afraid without carefully studying your
simulation.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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