[gmx-users] About g_msd

[Justin A. Lemkul]

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> Justin A. Lemkul wrote:
> > Hi Alan,
> >
> > Thanks for the reply.  My initial trajectory showed several of the lipids
> jumped
> > across the box and continued through the bilayer from there, which resulted
> in a
> > large displacement, so I processed the trajectory with trjconv -pbc nojump.
> > There is still a rather large initial displacement (within the first
> several
> > nanoseconds out of 100, likely due to my equilibration procedure of packing
> the
> > lipids tightly around the peptide), so I attempted to analyze the last 75
> ns and
> > 90 ns of the trajectory, using the structures at those times as the
> reference
> > (in g_msd -s).  Still the same result, a large value of D.
> >
> > Any ideas?
>
> please go back to your original trajectory and do normal g_msd for the P
> atoms only. (no mol flags etc.)

Thank you!  This appears to be giving me reasonable results.  I have several
dozen more trajectories to analyze, and will report back if anything goes
amiss, but so far it's a good start!

-Justin

> >
> > Thanks again.
> >
> > -Justin
> >
> >
> > Quoting Alan Dodd <anoddlad at yahoo.com>:
> >
> >> 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.
> >> 76.
> >>
> >> 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
> >> message.
> >>
> >> -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/
> >>
> >> ========================================
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> >>
> >>
> >>
> >>
> >
>
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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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>
>
> --
> David van der Spoel, Ph.D.
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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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/

========================================