[gmx-users] diffusion of oxygen in water
Mark.Abraham at anu.edu.au
Thu Jan 1 11:51:42 CET 2009
Sunil Thapa wrote:
> RESPECTABLE EXPERTS
> HAPPY NEW YEAR
Please don't use all capitals - it's the internet equivalent of shouting.
> I am a beginner in gromacs. I want to know if it is possible to study
> the diffusion of oxygen (as solute ) gas in water (solvent) with the
> current features of gromacs.
Yes, it's possible.
> Does gromacs present the required forcefields?
I highly doubt the standard forcefields are suitable for it. One needs
to have parameters that reproduce suitable existing data before one can
use them in a simulation for finding unknown data. A simulation such as
you suggest would not have many common features with the kinds of
simulations done with the standard forcefields, and any such
extrapolation would be likely to be a very questionable practice.
> How can I make the corresponding pdb file for oxygen as solute?
genbox probably works, but you need to identify a suitable forcefield
before it's relevant.
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