Hello, Does anyone have additional details about how the calculations are done for the -mol flag of g_msd when using -rmcomm? I am comparing results with and without the -mol flag. I presume that when -mol is used the file specified by the -o flag contains the average msd of the centers of mass of the molecules chosen with the index group and when -mol is not used, -o contains the average msd of atoms in the selected group.
I have two specific questions: (1) Why would the msd of the COM of molecules be greater than the msd of the atoms at low dt (or at all length scales in some cases)? This does not happen when -rmcomm is not used but then the diffusion is wrong (too fast). (2) Why does the -mol msd curve up along a vertical asymtote at tmax when using -rmcomm? My system is a mixture of lipids in a bilayer run for 200 ns where COM of only the system was removed by mdrun. Trjconv was used to extract one leaflet of all lipids without water into an XTC file (e.g. upperleaflet-nojump.xtc). On this extracted sub-system, g_msd was run with -rmcomm and -lateral z while selecting for one lipid type with an index file. This was tried with and without -mol and comparing the outputs led to the questions above. Thanks, Matt ------------------------------------------------------- Matthew I. Hoopes, Ph.D. Candidate Biophysics Graduate Group Department of Chemical Engineering and Material Science University of California, Davis 3118 Bainer Hall 1 Shields Ave. Davis, CA 95616 mihoo...@ucdavis.edu 530-752-6452 ------------------------------------------------------- -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
