[gmx-users] Diffusion Coefficient

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Feb 18 01:05:01 CET 2004

>I want to calculate the diffusion coefficient of water near and far from
>the protein and I have Root mean square deviation(RMSD)graph but dont know
>how to calculate dissusion coefficient from it. So please help me out. Is
>there any other way to calculate diffusion coefficient using
>gromacs?Please let me know as early as possible as It is quite urgent.

All the programs/scripts that come with GROMACS are detailed in the manual, 
indicating what they can do and how to do it.  In your case, you want to 
use g_msd: http://www.gromacs.org/documentation/reference_3.2/online/g_msd.html

Since you have two different regions you want to determine the value you 
for, I suspect you will have to generate an index file with a group for 
each of those regions of water molecules.  Should be something to do that 
in the programs/scripts as well.

Catch ya,

Dr. Dallas Warren
Research Fellow
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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