[gmx-users] diffusivity computations

[David van der Spoel]

Debashis Dutta wrote:
> Hi all,
>       I have been trying to estimate the diffusivity of an alanine 
> molecule in water with the .mdp file (for md simualtions) given below.
> 
> When I plot the mean square displacement, however I do not see a linear 
> variation with time (which is what I expected). Moreover, the estimated 
> diffusivity (using the g_msd command) looks reasonable (1e-5 cm^2/s) for 
> runs shorter than 0.1 ns. If I run it further, the diffusivity keeps 
> increasing to values of 1e-3 cm^2/s (for 10 ns runs). Any comments or 
> sugestions?
> 
since you only have one molecule expect to see very nosiy curves. you'll 
have to do 10-100 simulation to measure
this accurately.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. 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://folding.bmc.uu.se
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