[gmx-users] diffusivity computations

David van der Spoel spoel at xray.bmc.uu.se
Wed Jun 14 22:53:38 CEST 2006

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 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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