Re: Pressure problem to equilibrate NPT

From: Aron Broom (
Date: Mon Oct 22 2012 - 21:14:42 CDT

You can't change pressure without changing volume at the same temperature.
Is this what you are hoping to find? Keep in mind that approximately
speaking PV=nRT.

If you feel the need to heat, you should heat with NTP from 0 to 300K with
the pressure kept constant. Or, energy minimize extensively first, and
then just start your system at 300K with the pressure you want. Keep in
mind that the solvation of your system is usually done with
pre-equilibrated water, that should be pretty close to reasonable for 300K
and 1 atm.

Also, are you using the default pressure parameters? If something is going
wrong, I would use the defaults unless you have specific reason not to.


On Mon, Oct 22, 2012 at 6:28 PM, Mariana Graterol <
> wrote:

> Dear Namd user's:
> I want to equilibrate my system: protein + ions + box of water, at 300
> K and 1 atm. I solvated, minimized and heating in stages: first at
> 100K, at this point I had equilibrate the volume of my box, and then I
> continue heating to reach 300 K.
> After heating at 300 K; with a volume 1023339.8402 AA˄3, to give a
> density of 1.02369 g/cm^3, the PRESSAVG is around 5188.8741 Bar.
> To tranquilizer my system at 300 K, I run NPT dynamics, with the
> following parameters to control pressure:
> # Constant Pressure Control
> useGroupPressure no
> useFlexibleCell no
> useConstantArea no
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 800
> langevinPistonDecay 400
> langevinPistonTemp 300
> I simply got a relax in pressure at expense of volume! (the volume
> increases until 1500000 bar aprox.) I cannot really control pressure
> with the piston to progressively relax at my new temperature, without
> affecting my volume value (and density).
> Sorry for continuing asking, I am new with molecular dynamics an NAMD,
> How can I equilibrate pressure properly? With values less of 800 and
> 400 of piston period and piston decay, respectively, I got the error
> UNSTABLE SIMULATION, atoms moving too fast.
> Thanks very much for your time, to read this.
> Sincerely,
> Mariana
> --
> * mari *

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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