[gmx-users] About g_msd

Alan Dodd anoddlad at yahoo.com
Wed Jan 16 02:01:46 CET 2008

What happens if you visualise the trajectory?  Two orders of magnitude in scale of lipid movement should stick out like a sore thumb.

----- Original Message ----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Wednesday, January 16, 2008 12:27:45 AM
Subject: [gmx-users] About g_msd

Hello again,

I'm back with a few more questions about g_msd (version 3.3, in case I hadn't
mentioned that before).  Thanks to Xavier's message earlier, I have abandoned
use of ordered trajectories to analyze my lipids.  I will deal with lipid
"shells" in the future.  For now I am approaching the problem of lateral
diffusion coefficients from a slightly different angle.

My system contains a helical peptide that is oriented asymmetrically with
respect to the DPPC bilayer.  It is tilted and only partially embedded into the
intracellular leaflet of the bilayer (at the beginning of the simulation).  Due
to the asymmetry, I would like to study the properties of the leaflets
separately, including, among other parameters, the lateral diffusion
coefficients of the component lipids.

I have found a few papers that have simulated pure DPPC bilayers, and am using
them as somewhat of a reference point for the magnitude of the lateral
diffusion coefficients that I am determining:  E. Lindahl and O. Edholm (2001)
J. Chem. Phys. 115 (10), and U. Essmann and M. L. Berkowitz (1999) Biophys. J.

For the top leaflet of my bilayer, I am getting a value of D = (4.0+/-2.2)x10^-7
cm^2/sec (reasonable, in terms of order of magnitude, I think), but for the
bottom leaflet, I am getting roughly (355.7+/-551.5)x10^-7 cm^2/sec.  I figured
this enormous number was due to artefacts of PBC, so I tried every iteration of
trjconv -pbc, but to no avail.  Every result is quite similar.  I tried
starting g_msd at a later time (10 ns, 25 ns) to determine if any large initial
movements of lipids were responsible for the result, but I'm still coming up
with the enormous value of D (albeit slightly lower, ~200+/-400)

I am using g_msd -mol, with an index file that contains molecule numbers, and
then using g_analyze on the output .xvg file to get the values of D.

Has anyone ever experienced anything similar?  Am I missing something obvious?

Thanks in advance, as always, especially if you read the entirety of my lengthy



Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080

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