[gmx-users] g_msd

Borys Szefczyk szefczyk at mml.ch.pwr.wroc.pl
Mon Apr 20 10:53:03 CEST 2009

Dear Gromacs users,

I'm doing some tests on molten sodium chloride, trying to calculate
self-diffusion coefficients of both ions. Could someone tell me what
actually does the -ngroup switch of the g_msd program?

When I compute D for chlorine only, I get 6.4607e-5 cm^2/s;
for sodium only, I get D = 9.0996e-5 cm^2/s.

But when I set -ngroup to 2 and specify both groups (NA and CL)
subsequently, I get:
D[       NA+] = 9.0976e-5 cm^2/s
D[       CL-] = 0.9128e-5 cm^2/s
Plot of MSD looks fine for NA, but not for CL - it's a saw-shaped,
almost flat line.

If I enter the groups in reverse order, first CL, then NA, I get:
D[       CL-] = 6.4607e-5 cm^2/s
D[       NA+] = 4.2326e-5 cm^2/s
Again, first plot look fine, the second - not.

Why these results differ?

Borys Szefczyk

                 REQUIMTE,  &  Molecular Modelling & Quantum Chemistry Group,
  Department of Chemistry,  &  Institute of Physical & Theoretical Chemistry,
       Faculty of Science,  &  Wroclaw University of Technology
       University of Porto  &  http://ichfit.ch.pwr.wroc.pl/people/szefczyk

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