Re: Simulating air with NAMD

From: JC Gumbart (
Date: Sun May 06 2007 - 21:14:56 CDT

Well, by gas phase, what you mean, and I think may not be clear to
some people, is that it is essentially simulating the (presumed)
protein in a vacuum. This is done sometimes, I'm sure, and may be
reasonable. But he didn't say WHAT he was simulating other than air,
so I only addressed that particular part of the question. :)

On May 6, 2007, at 8:18 PM, 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.
> Mark

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