[gmx-users] diffusion of oxygen in water

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jan 1 11:51:42 CET 2009

Sunil Thapa wrote:

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.


More information about the gromacs.org_gmx-users mailing list