RE: AMBER: The pressure

From: Ross Walker <>
Date: Tue, 8 Mar 2005 18:20:44 -0800

Dear Bo,

> I have a few production runs on my structure model. The
> average pressures
> are various. One is about 2 atmosphere, the other is about 5
> atmosphere.

> The energy (total, potential and kinetic) levels remain in
> stable levels.
> The RMSd values for these simulation are also quite stable (~1.2
> average). With these high average presseure levels, am I still able to
> say that the MD simulations are resonalble? I use Amber7. The systems
> were solvated with WATBOX TIP216 at 10A thickness.

Can I see your input files. Are you running constant pressure periodic
boundary conditions? What are the values of NTB, NTP and PRES0 and TAUP?
Ideally the average pressure of your system should approach PRES0, however,
it is possible that your system is either: a) not sufficiently equilibrated
b) the run is too short for accurate statistics, or you dump to the output
file too infrequently, c) you have some kind of restraints defined which
stop the pressure regulation working correctly.

Your calculations are only really in question if case a is the situation.
Try plotting the average pressure as a function of time (you can use a
moving box car average for this) and see if it is converging over time, this
will give you an idea of whether your system is sufficiently equilibrated.
You could also take a look at volume as a function of time as this is
loosely related to the pressure. E.g. if your volume is continuously falling
your pressure will most likely be continually rising.

If you have restraints on your system then, I think, the regulation of
pressure will be affected by this and so you may not converge to the value
of pres0.

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 Wed Mar 09 2005 - 02:53:01 PST
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