Re: Namd water density

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Sep 23 2008 - 23:11:11 CDT

Hi Jouko,
a potentially incomplete list of things to look at:
-run more than 25 ps -- the uncertainty in your average will be huge
with such a short simulation
-use a thermostat if you're using a barostat
-use a temperature above the freezing point of water (MD water models
aren't designed to handle this phase transition)
-note that even if you do all of these things, the densities obtained
from MD simulations won't exactly match physical values (particularly if
you use pme -- see, eg, Price and Brooks III, JCP 121:10096--10103
(2004)). Using a pme-corrected water model may help with this, but they
haven't in general been tested as thoroughly

jouko_at_uchicago.edu wrote:
> I am running a simulation of a water box using Nose-Hoover
> Langeving piston pressure control. I have averaged the
> simulation box volume from the output file and calculated the
> density. The density is 0.351 e/A^3. It should be 0.334
> e/A^3. I am attaching my configuration file. Any ideas as to
> what is going wrong will be appreciated.
>
>
>
> Thanks,
>
> Jouko
>

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