[gmx-users] Organic Solvents
spoel at xray.bmc.uu.se
Wed Mar 2 20:41:10 CET 2005
On Wed, 2005-03-02 at 15:34 -0400, Anthony Cruz wrote:
> Thank you for the responce.
> I also have a question. It is possible to run an MD with two different FF, one
> for the solvent and another for the protein?
Not recommended unless you want to explicitly test the stuff yourself.
Otherwise referees will complain.
> On Wednesday 02 March 2005 03:49, David van der Spoel wrote:
> > On Wed, 2005-03-02 at 09:01 +1100, Dallas Warren wrote:
> > > > In the case of of creating a new one for example dioxane which could
> > > > be the
> > > > procedure? Something like this?
> > > > 1. make the topology in the PRODRG server.
> > > > 2. make a box and filled with the new solvent.
> > > > 3. equilibrate the box
> > > > This procedure is correct??
> > >
> > > Then run a simulation and check that its physical properties reproduce
> > > experimental values. Such as density, enthalpy of vapourisation,
> > > dielectric constant etc.
> > Indeed.
> > Do also check that the parameters are compatible with the force field
> > you'd want to use. OPLS has many parameters for organic molecules (check
> > ffoplsaa.atp)
> > > Catch ya,
> > >
> > >
> > > Dr. Dallas Warren
> > > Lecturer
> > > Department of Pharmaceutical Biology and Pharmacology
> > > Victorian College of Pharmacy, Monash University
> > > 381 Royal Parade, Parkville VIC 3010
> > > dallas.warren at vcp.monash.edu.au
> > > +61 3 9903 9083
> > > -------------------------------------------------------------------------
> > >- When the only tool you own is a hammer, every problem begins to
> > > resemble a nail.
> > >
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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