[gmx-users] About g_msd

[Justin A. Lemkul]

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

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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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