Pressure problem to equilibrate NPT

From: Mariana Graterol (
Date: Mon Oct 22 2012 - 17:28:55 CDT

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.



* mari *

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