[gmx-users] About g_msd

Wed Jan 16 09:41:51 CET 2008

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 <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/
> 
> ========================================
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-- 
_______________________________________________________
Patrick FUCHS
Equipe de Bioinformatique Genomique et Moleculaire
INSERM U726, Universite Paris 7
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