Re: Solvent mixture

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Nov 05 2004 - 16:53:11 CST

All my work with cosolvents used in house md codes and parameters. I
haven't transfered them to a charmm format as yet.
Brian

On Fri, 5 Nov 2004, Edward Patrick Obrien wrote:

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

*****************************************************************
**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 **
*****************************************************************

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:27 CST