From: Rajan Vatassery (rajan_at_umn.edu)
Date: Mon Nov 14 2011 - 01:14:41 CST
Dear Jeffrey and Johan,
Thank you for your input. As you had likely suspected, I made a mistake
converting the sigma values from the Chem Phys paper to Rmin/2. The
correct parameters in Rmin/2 format are:
C and Cl: 1.880 Angstroms
H: 1.543 Angs
The other paper's parameters were apparently incorrect, in that they did
not reproduce a correct pressure at a proper density of CH2Cl2.
From the simulations where I tried to get the density to match
experiment, it seems like the Chem Phys paper is slightly high still,
but it's possible that it will be close enough. I would consider this
problem solved, and thanks again for your help.
rajan
On Tue, 2011-11-08 at 22:13 -0500, johan strumpfer wrote:
> Hi Rajan,
>
> I've had a similar problem with a glycerol/water mixture. For me it
> came down to a poor initial construction that required multiple NVT +
> minimization cycles (total NVT simulation time was about 10 ns if I
> remember correctly) to get the simulation box to roughly the right
> volume before turning on the barostat and starting equilibration.
>
> I considered also starting with a low pressure system (to allow easier
> reorientation of the molecules) and slowly increasing the pressure to
> the required value. I ended up not needing to try it, but you may want
> to give it a shot.
>
> First make sure that you're force field parameters (and relevant namd
> config options) are correct, then you can try the above procedures.
>
> Cheers,
> Johan
>
> ------------------------------------------------------------------------------------------------------
> Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
> Theoretical and Computational Biophysics Group
> 3115 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801, USA
> ------------------------------------------------------------------------------------------------------
>
>
>
> On Tue, Nov 8, 2011 at 9:43 PM, Rajan Vatassery <rajan_at_umn.edu> wrote:
> > 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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