Re: phase equilibria using NAMD

From: Brian Bennion (
Date: Thu Jul 22 2004 - 10:53:00 CDT

Hello Nasrat,

Can you say how big your systems of each compound are?
Small system sizes will give greater fluctuations around a mean value
be it pressure or temperature.
Its hoped that the mean value doesn't change much over the simulation.
Moreover, the system size needs to be larger than your cutoffs and your
cutoff values should be sufficient to capture important interactions. For
nonpolar uncharged systems the electrostatics might need more than 10A
because of the relatively low charge screening (low dielectric). Nonpolar
interactions (ie Lennard Jones type) will all be captured by 10A cutoff.

The greatest source of error will be your van der Waals parameters and
partial charges that describe your solvents(solutes?) I am assuming that
these systems are homogenous.

Could you explain what you mean by tail correction?


 On Wed, 21 Jul 2004, nasrat kamal wrote:

> Hello,

I am using NAMD to perform simple MD simulations in NPT ensemble to calculate equation of state,
phase equilibria and other thermodynamic properties of isobutane, isobutene and N-methyl-2-pyrrolidon.
I have estimated phase equilibria for NMP but the critical point is coming out to be 100 K lower than the experimentally obserbed value.
This can happen if the expression for tail correction (due to truncation of potential) is not included while calculating pressure and energy.
Does anyone knows if NAMD also incorporates tail correction in the simulations? If not, then how can we include that?
I have already performed simulations and I would also like to know if I can incorporate the corrections directly to the results.

Also, in NPT ensemble simulations, the pressure is not at all constant, but shows fluctuations upto +-1000 bars. Does this means that there is something wrong in the simulations ??

Looking forward for your help,
Many thanks,


**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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