Re: Negative Pressure

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed May 07 2008 - 09:39:02 CDT

Dear Fabio,

Presumably you start with a non-equilibrated system which occupies a
larger volume that it needs too (low density). Therefore, initially your
pressure will have large negative values (which just means that your
system volume needs to shrink). In the average P, the initial phase of
adjusting the volume will also be included, thus explaining you negative
average pressure.

What is the average P over the last 500 ps?? That should converge to 1
if your system is well equilibrated. Note that the instantaneous P shows
large fluctuations (as discussed many many times on this list and other
MD docus)

I usually equilibrate with LangevinHydrogen turned on (without rigid
bonds). I am not sure how "LangevinHydrogen off" would affect velocity
distribution ... I believe your systems appears colder when using
LangevinHydrogen off ... You can test that by doing a restart (include
velocities or binvelocities from a previous run) and check the T at step
0 (which should be 300 if well equilibrated).

Best
vlad

 Fabio Zegarra wrote:
> Dear NAMD users:
>
> I am equilibrating a small protein (NPT simulation , 1 nanosecond).
> The protein is in a water box (with around 8000 water molecules) with
> periodic boundary conditions, and I am using the following parameters
> to control the temperature and pressure.
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp 300
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> # Constant Pressure Control
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
>
> To check the simulation I calculated the average temperature and
> pressure in the *.log file, the average temperature is around 299 K,
> but the average pressure is around -20 bar . To make sure I also used
> other parameter values, but the results were the same (negative
> average pressure). I want to know if this is right or I have to change
> something in the control parameters.
>
> Sincerely,
> Fabio

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