From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Feb 20 2009 - 10:09:52 CST
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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