[gmx-users] Organic Solvents

[David van der Spoel]

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.
________________________________________________________________________
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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