[gmx-users] Diffusion Coefficient

Erik Lindahl lindahl at csb.stanford.edu
Wed Feb 18 01:20:02 CET 2004


Check the documentation of g_msd  (on the web, or "g_msd -h", or "man  
g_msd") - it will even do the fitting automatically for you and  
calculate the diffusion coefficient.

For reference, under self-diffusion the mean square displacement (MSD)  
is proportional to 2*N*D*t, where N is the number of dimensions (e.g. 2  
in a plane, 3 in free space), D the diffusion coefficient and t time.

Since you always have a region of "free flight" for very short times it  
is best to calculate the slope of the MSD (starting at t>0) instead of  
approximating it as a strict proportionality.



On Feb 17, 2004, at 11:40 PM, Dallas Warren wrote:

>> 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
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