RE: AMBER: Amber8: Vlimit problem again

From: Ross Walker <>
Date: Wed, 21 Jul 2004 16:55:59 -0700

Dear Yuhui

> Can I turn off shake and set dt=0.0005? Actually,

Yes, this may or may not fix your problem though. You may need to do some
Minimisation followed by equilibration at a low temperature, possibly with
some restraints
on the unstable bit, then you can gradually relax the restraints and
increase the temperature.
You will have to experiment.
> my simulation system should be instable since it's the
> product complex and the phosphorylated peptide should
> be released. Is it possible that the high fluctuation
> of the product peptide results in such a problem?

Why don't you try getting it to write you an mdcrd file more frequently.
Every step is good if you have the disk space. Set ntwx=1 and ntpr=1. In
this way you will be able to monitor the system at every step. Then try
visualising the mdcrd file in something like VMD and you should be able to
see what is causing your system to blow up. Once you know this you can take
informed steps to prevent it.

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 Thu Jul 22 2004 - 01:53:00 PDT
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