Hi all, I have 100-ns trajectories of a membrane protein embedded in a lipid bilayer and I am trying to compute the lateral diffusion coefficients of the lipids in different "shells" around the protein. Everything was going fine until I re-checked the documentation, at which point I got a little confused. Can someone please help me sort out what I need to do to get the correct lateral diffusion coefficients of my lipids?
I have an ordered trajectory (from trjorder), with the lipids ordered according to their distance from the protein. When I issue the command: g_msd -f ../../TrajFiles/ordered.xtc -s ../md.tpr -n ../lipids_shells.ndx -o msd_shells.xvg -ngroup 4 -lateral y -trestart 1000 (and subsequently selecting each of my four index groups) I get output of lateral diffusion coefficients for each group. The index group specified has the lipids by their molecule number, which brings me to my first question: Is that the proper index group to use if I am not specifying -mol? Some of my results come up negative, and I see from the archive from DvdS that this is due to poor single molecule statistics, but I my index file specifies multiple molecules in a shell. I suspect this is a problem with the index file? Do I have to specify the desired group in terms of all the atoms in the lipids of interest? When I issue: g_msd -f ../../TrajFiles/ordered.xtc -s ../md.tpr -n ../lipids_shells.ndx -o msd_shells.xvg -mol msd_mol_shells.xvg -ngroup 4 -lateral y -trestart 1000 (please note the use of the same index file) I get a very different result. The lateral diffusion coefficients in msd_shells.xvg are two orders of magnitude larger than in the first result, and the msd_mol_shells.xvg is filled with mostly 'nan' entries. Is this because of some incompatibility between -ngroup and -mol? I have found in the list archives that the number without the -mol option is more accurate due to statistical sampling, but that seems to contradicts the manual entry for g_msd. Hence my confusion. Thanks in advance for any comments and hints. -Justin ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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