RE: AMBER: density problem

From: Ross Walker <>
Date: Tue, 31 May 2005 08:33:39 -0700

Dear Cristian,

> disappear. I try to set taup=0.1 but even in this manner it does not
> function. These strange holes were created in the previous
> heat up step.

I assume you heated with constant volume. I find that initially heating with
constant volume from a LEaP solvated system can cause problems because you
get these very large voids form that are hard to get rid of. However,
pressure calculations are unreliable at low temperatures so initially
starting out with constant pressure can cause problems. What I would do is
do a very short run (2ps or less) to heat your system up with constant
volume to 100K or so and then switch to constant pressure. This will allow
the voids created by LEaP to be filled and you should then see your pressure
equilibrate around 1 atm. Once your pressure has equilibrated you can either
switch back to constant volume ro stay at constant pressure.

I hope this helps.
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 Tue May 31 2005 - 16:53:03 PDT
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