AMBER Archive (2003)

Subject: Re: AMBER: problems with pressure control

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 30 2003 - 12:03:06 CST

On Tue, Dec 30, 2003, Endres, Robert G. wrote:

> I have some difficulties with constant pressure MD runs. The system is a
> solvated molecule inside a box with periodic boundary conditions. After
> equilibration at 300K with constant volume, I wanted to run at constant
> pressure. When I choose the default target pressure pres0=1.0 [atm] then the
> VOLUME of the box slightly shrinks during MD using input
>
> The PRESS variable in output file starts correspondingly negative (-654.0),
> and converges to zero. However, when I choose pres0=0.0 for gas phase, the
> box still shrinks although less strongly. I would have expected that the
> system would expand at zero applied pressure at 300K (?) I also tried a
> negative target pressure pres0 which surprisingly didn't give an error
> message and still led to a slight shrinking of the box. Does anyone
> understand how the pressure control works (in particular at low pressures)?
>

It can take a really long time to equilibrate to the final density. If you
start with a system of about the correct density for atmospheric pressure,
that may converge relatively quickly. But if you then set the external
pressure to zero, and want the system to expand to some other final
density, that will probably take a macroscopic amount of time, i.e.
simulations that are far longer than you could ever afford to do.

The main problem here is that water very strongly self-associates, so that
the kinetic process of breaking water-water interactions is very slow. If
you were to study a rare-gas, on the other hand, you could follow its
pressure-density behavior in simulations of affordable times, since there the
atom-atom interactions are extremely weak, and hence are easily broken.

A few years ago, I used Amber to reproduce the equation of state for a LJ
fluid as shown, for example, in Fig.14-3 of McQuarrie's "Statistical
Mechanics"; this was an exercise to show that the program was working as it
should. Note that the equilibrium pressures are negative in parts of these
curves.

Simulations always explore the region of configuration space near where they
are begun. Studying large changes, such as phase transitions, require
specialized techniques, not supported in Amber. In particular, gas-phase
simulations are not very well supported.

..hope this helps...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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