From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Feb 23 2009 - 03:29:58 CST
did you read the link I sent earlier, and my comments about the need to
average over many steps?
Fred (Rui FENG) wrote:
> 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!
> On Fri, Feb 20, 2009 at 11:09 AM, Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto: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.
> 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>
> > <mailto: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
> > 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
> > value
> > > in this system after minimization? Thank you so much!
> > >
> > > Have a nice day!
> > >
> > > Fred
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