[gmx-users] Diffusion Coefficient

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 18 11:04:00 CET 2004

On Wed, 18 Feb 2004, 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.

trjorder dioes that.

>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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David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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