[gmx-users] About g_msd (and noise)

[Alan Dodd]

I've been playing with g_msd myself recently, and been seeing weird results toward the end of the simulation.  From the below post, it looks like I was doing it correctly (apart from analysing the leaflets separately).  Previous posts in the mailing list have implied that increased noise towards the end of a simulation is inherent in the algorithm, I just wanted to check that I was interpreting those posts correctly?  And if this is so, do people just not show the results towards the end?

----- Original Message ----
From: David van der Spoel <spoel at xray.bmc.uu.se>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Wednesday, January 16, 2008 6:48:32 AM
Subject: Re: [gmx-users] About g_msd

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.)
> 
> 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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