Justin A. Lemkul jalemkul at vt.edu
Sun Jan 13 04:08:10 CET 2008

```Xavier,

Thanks for the reply.  I'm running of analysis now on my original, non-ordered
trajectories.  I'll report back to the list with what I come up with.

-Justin

Quoting Xavier Periole <X.Periole at rug.nl>:

> 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
> >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.
>
> 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
> protein.
> 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.
>
> XAvier
>
> >
> > 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.
> >
> >
> > -Justin
> >
> > ========================================
> >
> > Justin A. Lemkul
> > 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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> -----------------------------------------------------
> XAvier Periole - PhD
>
> NMR & Molecular Dynamics Group
> University of Groningen
> The Netherlands
> http://md.chem.rug.nl/~periole
> -----------------------------------------------------
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========================================

Justin A. Lemkul