[gmx-users] Organic Solvents

[Anthony Cruz]

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?


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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