RE: AMBER: AMBER 8 : Water cap problem

From: Ross Walker <>
Date: Mon, 14 Feb 2005 09:07:21 -0800

Dear Bollot

> I have a problem in molecular dynamic simulation on a protein
> and water cap.
> My problem is that one or two water molecules had extended beyond the
> extent of the virtual box (Error message).
> I restarted(IREST=1, NTX=5) my dynamic but the problem is the same.
> Are there some solutions at this problem?
> Thanks in advance.

Check the cap force fcap. It may be zero or may need to be increased.
Secondly try viewing the trajectory. For a water molecule to leave the
virtual box during a water cap simulation would require a lot of energy if
the cap force is greater than zero.

It is possible your system is unstable and blowing up. Watch the trajectory
in something like VMD and this should be obvious. If this is true then you
may need to be more careful in your simulation. Minimise the system better
and heat it more slowly.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Mon Feb 14 2005 - 17:53:01 PST
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