[gmx-users] g_msd

[Yanmei Song]

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?
>
> Regards,
> 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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-- 
Yanmei Song
Department of Chemical Engineering
ASU