[gmx-users] MSD again

Periole Xavier periole at inka.mssm.edu
Tue Feb 12 22:27:18 CET 2002

Hi Lars,

I didn't follow the previous emails but you are probably
trying to calculate the diffusion constant of the molecule
of oxygen.

My experience of this kind of calculation make me think
(I didn't check the manual, but ...) that the two plots actually
are the msd in two different ways. One, from g_msd, is probably
the instantaneous value of the msd, the other, from g_analysis, is
(a average over the simulation of) the msd obtained for a given
duration of simulation. The last is (probably) what you are interested
in, meaning the one from which you are going to be able to extract
the diffusion constant, D, using the relation :

lim {[r(t0)-r(t)]**2} (t-> infinity) = 6 * D *t  (see page 140
of the manual of gromacs and the curve page 141).

The curve obtained with g_analysis, is a plot of a average,
over the whole simulation, of the msd ([delta r]**2) in function
of (delta t)s in your simulation or t in general. Practically the
(delta t) is chosen (e.g. 10 ps), you calculate the msd positioning
the t0 at several time of the simulation (e.g. 1ps, 2ps, 3ps, ... you
choose the space between those values probably using the -trestart
option in g_msd) and you average the values of the msd. This
way you have your msd for the (delta t)=10ps (or t). You do it
again for (delta t)=20ps, 30ps, 40ps, ... and you reach the
plot you have from g_analysis. That is the msd=f(t) from which
you get your D: 6*D=(delta r^2)/(delta t).
The plot stops at half simulation, because it's consider that the
becomes too poor for using t (or delta t) bigger than half of the
simulation. The person who wrote the program though for the

By the way, you should be able to obtain the same curve using
g_msd with the option "-mol" ??? not sure ... perhaps directlly the
D value. The curve you have from g_msd is the one that brings
you to the one obtained by g_analysis.

I hope it'll help you,

Xavier Periole
Department of Physiology and Biophysics
Mount Sinai School of Medicine
One Gustave L. Levy Place
New York, NY 10029-6574
Tel:  (212) 241-8192
Fax: (212) 860-3369
E-mail: periole at inka.mssm.edu

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