[gmx-users] About g_msd

[Justin A. Lemkul]

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?

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

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/

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