Re: Can I get the pressure value in a cube?

From: Fred (Rui FENG) (fengruifree_at_gmail.com)
Date: Mon Feb 23 2009 - 00:57:29 CST

Hi Peter,

Thank you for your help. I successfully made the pressure output.

Now I'm trying to get the pressure of the Apoa1. Its PDB, PSF, parameter
files, and the configure file are provided by NAMD group. You can get it
here: http://www.ks.uiuc.edu/Research/namd/performance.html I think you may
be quite familiar with it.

When I run the code and get the output (see below), I found the pressure
value is weird. It's a small negative number (-5241). I think the pressure
inside the box should be close to 1 bar. Could you tell me why it's so small
here? Thank you so much!

ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY
MISC KINETIC TOTAL TEMP
TOTAL2 TOTAL3 TEMPAVG PRESSURE
GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 200 21073.6837 18595.6349 5711.8747
190.0258 -334670.2812 21209.9247 0.0000
0.0000 45319.1601 -222569.9773 164.8586 -222233.3648
-222114.5247 164.8586 -5241.8526 -2703.6813
921491.4634 -5241.8526 -2703.6813
Have a nice day!

Fred

On Fri, Feb 20, 2009 at 11:09 AM, Peter Freddolino <petefred_at_ks.uiuc.edu>wrote:

> You need to get the pressure output from real MD steps... try adding
> run 0
> to the end of your config file.
> Peter
>
> Fred (Rui FENG) wrote:
> > Hi Peter,
> >
> > In my simulation I fix the volume. The output of the pressure during
> > minimization is just 0. It's also the same when I comment off the
> > minimization. It looks like this:
> >
> > PRESSURE: 200 0 0 0 0 0 0 0 0 0
> > GPRESSURE: 200 0 0 0 0 0 0 0 0 0
> > Do you think I should turn on other parameters? Thank you!
> >
> > Have a nice day!
> >
> > Fred
> >
> > On Thu, Feb 19, 2009 at 11:26 PM, Peter Freddolino <petefred_at_ks.uiuc.edu
> > <mailto:petefred_at_ks.uiuc.edu>> wrote:
> >
> > There is, in fact, a pressure output field in the namd logfile that
> you
> > may want to look at. However, it is only meaningful to look at the
> > pressure averaged over a (moderately long) MD run. See
> > http://www.ks.uiuc.edu/Research/namd/2.6/ug/node32.html or a
> statmech
> > textbook for why.
> >
> > Peter
> >
> > Fred (Rui FENG) wrote:
> > > Hi All,
> > >
> > > I set up a cube with periodic boundary condition. I put thousands
> of
> > > particles inside and set up sigma and epsilon for Lennard Jones
> > > Potential parameters (VDW). There's no bond between particles. The
> > only
> > > force field between them is Lennard Jones. Can I get the pressure
> > value
> > > in this system after minimization? Thank you so much!
> > >
> > > Have a nice day!
> > >
> > > Fred
> >
> >
>

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