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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
