ysong30 at asu.edu
Mon Apr 20 18:00:45 CEST 2009
I had the same problem before. I think the best way to do it is to
analyze every group separately.
On Mon, Apr 20, 2009 at 1:53 AM, Borys Szefczyk
<szefczyk at mml.ch.pwr.wroc.pl> wrote:
> 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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