Re: Pressure Problems, Excessively High Readings

From: johan strumpfer (
Date: Tue Nov 08 2011 - 21:13:23 CST

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.


Johan Strumpfer:
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 <> 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
>        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:
> 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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:54 CST