Re: Solvent mixture

From: Ahmet Bakan (bakanku_at_gmail.com)
Date: Fri Nov 05 2004 - 17:02:06 CST

Hi Ed,

I had studied on dimethyl urea (DMU) compounds a year ago. I have a
topology of DMU on my web page. I hope it may help you to creat an
urea topology.

http://home.ku.edu.tr/~abakan

Cheers,
Ahmet

On Fri, 5 Nov 2004 17:43:21 -0500 (EST), Edward Patrick Obrien
<edobrien_at_glue.umd.edu> 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 **
> > *****************************************************************
> >
> >
>
>

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