Re: Solvent mixture

From: Brian Bennion (
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


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 **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **

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