Re: Solvent mixture

From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Fri Nov 05 2004 - 16:43:21 CST

Hi Brian and Sepp,
  I've never been able to find Urea parameter/topology in CHARMM format,
have either of you?

  If so, could you let me know how I can get these files.

Thanks,
Ed

On Fri, 5 Nov 2004, Brian Bennion wrote:

>
> 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 **
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