Re: Simulating air with NAMD

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun May 06 2007 - 19:09:03 CDT

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.

On May 6, 2007, at 2:37 PM, JC Gumbart wrote:

> For what purpose do you want to do this? I calculated at standard
> temp and pressure that you would only have 13489 molecules of ďairĒ
> in a cube 100 Ang on each side which would be pretty sparse. I
> donít think the CHARMM forcefield was parameterized for such
> simulations.
>
>
>
>
>
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Lechuga, Javier
> Sent: Sunday, May 06, 2007 10:05 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: Simulating air with NAMD
>
>
>
> Hello,
>
>
>
> How could I find a way to simulate air with NAMD?. I mean pdb, psf
> and prm files.
>
>
>
> Thank you
>
>

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