>>I am new to this newsgroup (and to MD). I would like to
>know if molecular dynamics can be used to estimate
>binary diffusion coefficients of A (solute) in B (solvent).
>Can X-Plor be used to do it? The system I am studying does not
>involve biomolecules, but small molecules (for example, benzyl
>chloride dissolved in toluene). Any pointers or suggestions
>regarding this would be much appreciated.
>
Yes MD can be used for that purpose. Diffusion constants are usualy
estimated from the slope of the displacement autocorrelation function
at longer time scale.
You can run free MD simulations with X-Plor. The only thing you have
to be aware of is that the current version only allows for constant
volume simulation (with or without periodic boundary conditions).
Cheers
Alexandre
==========================================================================
| Dr. Alexandre Bonvin | Phone: Int+41-1-632-5504 |
| Physical Chemistry, ETHZ | Fax: Int+41-1-632-1039 |
| Universitatstrasse 6 | Email: abonvin at igc.phys.chem.ethz.ch |
| 8092 Zurich, Switzerland | http://igc.chem.ethz.ch/abonvin |
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