From: Rajan Vatassery (rajan_at_umn.edu)
Date: Tue Nov 08 2011 - 20:43:10 CST
Dear NAMD-l,
I am trying to get an equilibrated box of CH2Cl2. I have a cubic box of
side length 95 angstroms, and I fill it with 4913 molecules. This works
out to be a lower density by a factor of 2/3 than the 1.33 g/cm^3 that
would be normal for CH2Cl2. I have minimized and equilibrated for more
than a nanosecond after a few brief increments of heating up the system
to 298 K. I have taken parameters from Chem. Eur. J. 2007, 13, 8139 –
8152, and also from Chemical Physics
72 (1982) 141-145 (separately). All relevant files and a few images are
located at http://www.tc.umn.edu/~rajan/NAMD-l.html
I get a very large pressure (350 bar) where the pressure really should
not be this high (it should be 1.01 bar). This is similar to these
peoples' problems:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12038.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1596.html
and a few others that I don't have at hand. In my case, the pressure
increased from -130 bar to 350 bar upon heating the system (100 K to
298) and I don't think it's an error due to a pathological portion of my
simulation because of the steady rise in this trend. I also tried
removing the PME portion of the calculation ("PME no"), but this did not
solve the problem. Could it be the case that my system is simply not
equilibrated? I looked at the log file and the pressure is not really
moving with each output step.
This is a problem because I need to equilibrate this solvent box at 1
atm and when I set the barostat to this setting, the system boils. It
almost seems like a unit conversion problem or something simple like
that. It looks like I'm not the only one experiencing it, although this
doesn't necessarily mean I'm not making a simple mistake.
Any help is greatly appreciated,
Rajan Vatassery
Department of Chemistry
University of Minnesota
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