Re: Problem equilibrating with low pressure

From: Mark Abraham (
Date: Sat Jul 01 2006 - 01:30:13 CDT

> Hi,
> I am trying to equilibrate a box of water at 300K
> and a very low pressure (0.05 bar). I need to
> calculate the density of the gas phase at this
> temperature. I used small pressure in order to allow
> the box to expand. I am using NPT simulation with NAMD
> using Langevin Piston method. I found that unless I
> use small values for the parameters
> LangevinPistonPeriod and LangevinPistonDecay, I can
> not control the pressure into such a small value. The
> water box has nearly 650 atoms and I tried to
> equilibrate for 250 ps.
> But if I do that, although the water box
> expands...the kinetic energy of the system is blowing
> up. I tried the same exercise at 350K and for a
> pressure equal to 0.1 bar and I see similar problem.
> And if I use a larger value for the parameters
> LangevinPistonPeriod and LangevinPistonDecay, the
> water box does not expand and the I get a very high
> pressure fluctuation.

Probably you are trying to do a jump in phase space that is too large for
numerical stability. Try a gradual regime of lowering the pressure with
equilibration at each increment. If you have an idea of the final volume,
you could also try starting with a box larger than that for 300K 1bar
water to accelerate the process.

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