[gmx-users] About g_msd (and noise)

Wed Jan 16 13:24:32 CET 2008

Alan Dodd wrote:
> 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?
> 

DESCRIPTION
-----------
g_msd computes the mean square displacement (MSD) of atoms from their 
initial
positions. This provides an easy way to compute the diffusion constant using
the Einstein relation. The time between additional starting points for the
MSD calculation is set with -trestart. The diffusion constant is calculated
by least squares fitting a straight line through the MSD from -beginfit to
-endfit. An error estimate given, which is the difference of the diffusion
coefficients obtained from fits over the two halfs of the fit interval.

Have you tried these option?

> ----- 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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>>
>>
>> ========================================
>>
>> 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