[gmx-users] MSD near specific molecules

[Jian Dai]

Dear users:
1. I have a lipid bilayer of POPC with cholesterols. I'm trying to calculate
the MSD of the POPCs which is nearest to cholesterols. The nearest POPCs are
defined as those POPC whose C13 atoms to O6 atoms from cholesterol distances
are less than a certain cutoff. Is there a good way to do that?
2. The overall lateral diffusion of each leaflet should be removed first.
Using GMX3.3.2, I intend to get it by using "trjconv -pbc nojump -center
-boxcenter tric", is that right?
3. The two leaflets have been separated, and if I apply g_dist to the groups
of  upper-cholesterol and upper-POPC, and then use g_analyze -msd, I can
only get the mutual diffusion of the center of mass of these two groups, is
that right?

Thank you.
-DJ
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