[gmx-users] About g_msd

Xavier Periole X.Periole at rug.nl
Sat Jan 12 11:31:08 CET 2008

On Fri, 11 Jan 2008 14:29:34 -0500
  "Justin A. Lemkul" <jalemkul at vt.edu> wrote:
> Hi all,
> I have 100-ns trajectories of a membrane protein embedded in a lipid bilayer 
> 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 
> to their distance from the protein.

The major problem I think you are facing is the fact that you use an
ordered trajectory. Then the lipids are ordered according to their
distance from the protein for each frame. This means that then in g_msd
you are analyzing discontinuous trajectory. g_msd considers that the
lipid number 2 is the same at each frame. In the ordered trajectory
the lipid number 2 might be going from one side to the other of the
In conclusion: you do not want to use an ordered trajectory to calculate
the msd of the lipids.
On thing you could do is cut the lipid trajectories in pieces depending
how far they are from the protein and then average over all pieces
of trajectories. The "large" unmber of trajectories might compensate
for their short length. Although for lipids you might actually have
simulations of reasonable length, as compare to water molecules.


> 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 
> specified has the lipids by their molecule number, which brings me to my 
> 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 
> this is due to poor single molecule statistics, but I my index file 
> 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 
> 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, 
> the msd_mol_shells.xvg is filled with mostly 'nan' entries.  Is this because 
> 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
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> ========================================
> _______________________________________________
> gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands

More information about the gromacs.org_gmx-users mailing list