Re: Simulating air with NAMD

From: Jeffrey J. Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Sun May 06 2007 - 21:38:35 CDT

On Mon, 7 May 2007, Mark Abraham wrote:

> JC Gumbart wrote:
>> Sorry, I just realized I was thinking 22.4 mol/L for air! Obviously, this
>> is too high, it's 22.4 L/mol at STP.
>>
>> No wonder my number seemed high. You will actually have 27 molecules in a
>> 100x100x100 Ang^3 box. That is pretty much impossible to simulate and
>> expect anything meaningful.
>
> Certainly impossible with a condensed-phase force field. However with
> non-bonded potentials optimized for gas-phase, I can't think of a principle
> that would be violated by such a simulation. Whether there exists such a
> force field already is a matter for a literature search, unless anybody
> already knows of such a thing.

The difficulty of the calculation depends what properties one wants
to get out of the the simulation, which the original poster has yet to
mention. Running an NPT simulation on air in NAMD is very easy. Force
fields for oxygen and nitrogen have been developed by chemsitry and
chemical engineering groups interested in PVT properties and phase
behavior of fluids. We published a force field for nitrogen that would
yield accurate gas phase results in [Potoff and Siepmann, AICHE J.
v47, 1676-1682, 2001]. I know someone else has done oxygen, and a
literature search should turn it up. These force fields are Lennard-Jones
+ point charge, and with a simple unit conversion can be used in NAMD in
place of CHARMM.

Regarding the size of the simulation box, if one is just running a
calculation on a bulk phase, one can get reliable results on systems with
as little as 100 molecules. Also, I would not expect someone simulating
air to do so at STP, where you have essentially ideal gas behavior.

Regards,
         Jeff

======================================================================
Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu
Associate Professor Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr Phone:(313)577-9357
Detroit, MI 48202 Fax: (313)577-3810
http://potoff1.eng.wayne.edu
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