Re: Solvent mixture

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Nov 05 2004 - 15:40:47 CST

I think this might have been discussed earlier on the list.
The hard part is getting the concentrations right by swapping waters with
cosolvent. I have used mole fractions for this purpose. Once you get a
box in pdb format it is trivial to get namd to run. This is if you have
already added the appropriate parameters and topologies to the charmm
files.

Regards
Brian

On Thu, 4 Nov 2004, Josef Scheiber wrote:

> Hi all,
>
> I want to perform a simulation using a defined mixture of water and urea as
> solvent. Does anybody have an idea, how to create such a solvent box, which can
> be used in NAMD?
>
> Thanks in advance,
> Sepp
>
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
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