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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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