RE: AMBER: constant pressure equillibration

From: Ross Walker <>
Date: Fri, 23 Jun 2006 08:53:17 -0700

Hi Simon,

> I am attempting to equilibrate my system (periodic with TIP3P waters)
> prior to running constant volume MD. However leap shows that
> the density
> of the water is 0.85 g/cc. Therefore is it ok to, first run a
> period of
> equilibration with constant volume then switch on constant
> pressure when
> it is at temperature to bring the density to one then run the constant
> vol MD?

Yes this is a good idea. However, you don't want to run too long at constant
volume with an incorrect density or vacuum bubbles will start to form which
will take for ever to equilibrate out. However, you can't use constant
pressure while the temperature is low or the barostat correction could be
too large and blow the system up. Due to division by a small number when
calculating the pressure.

You have two options.

1) Do as you suggest and assuming you heat to 300K in less than 100ps or so
you should be okay and can then switch to constant pressure and until the
density has equilibrated, probably another 100ps or so but check it
carefully. Then you can switch back to constant volume and turn off the

2) If you want to heat more slowly I would suggest heating to about 50-100K,
then switch to constant pressure for the remainder of the heating. Once your
system is at the target temperature let it equilibrate here for a while. You
can then switch to constant volume give it bit more equilibration at the
target temperature and then finally switch off the thermostat for the
production run.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Jun 25 2006 - 06:07:19 PDT
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