Hi Justin,
Wohlert and Edholm (http://dx.doi.org/10.1063/1.2393240) suggested to
extract the motion of the 2 monolayers relative to each other, before
calculating the MSD. This is an artefact coming from the finite size of
computer simulations. This may explain the discrepancy you get between
both leaflets.
Second, they showed that there are two different diffusions. A fast
diffusion occuring on ps time scale and a longer one which is brownian
and can be compared to FRAP experiments. In their paper, they propose a
fitting procedure that extracts both diffusion constants. Furthermore,
be sure to equilibrate enough (a few tens of ns) before doing this analysis.
Cheers,
Patrick
Justin A. Lemkul a écrit :
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 <[EMAIL PROTECTED]>:
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 <[EMAIL PROTECTED]>
To: gmx-users@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
[EMAIL PROTECTED] | (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
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
========================================
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--
_______________________________________________________
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
Case Courrier 7113
2, place Jussieu, 75251 Paris Cedex 05, FRANCE
Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30
E-mail : [EMAIL PROTECTED]
Web Site: http://www.ebgm.jussieu.fr/~fuchs
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