Re: [gmx-users] g_msd and MSD analysis

[Dommert Florian]

On Sat, 2012-06-09 at 15:33 -0700, Mr Bernard Ramos wrote: 
 Hi everyone!
 
 
 I have a 20 ns  simulation (2fs timestep but coordinates saved every
 0.2 ps) and I was able to calculate the mean-square-displacement of
 the oxygen atoms of my water solvent. The entire MSD plot looks very
 linear to me. I need to fit this set of MSD data to obtain the
 diffusion coefficient. However, I am not sure if I will have to use
 the entire MSD points or may be just to consider a few picoseconds at
 the latter part of the simulation time. In papers I have read, they
 use up to a 100 ps, although no mention were made as to where those
 set of points came from.  Please help.
 

Hi,

have you looked at a linear graph or on a log-log representation. With
the latter representation, it is much easier to identify the different
regimes of diffusion (ballistic, subdiffusive, and linear). This should
allow you to chose an appropriate fit range. Moreover if you fit a
straight line to the log-log representation you will immediately see,
where the MSD curve deviates from the linear behaviour.

/Flo

 
 This post seems to suggest a nanosecond window for the analysis of the
 MSD curve
 
 
 http://lists.gromacs.org/pipermail/gmx-users/2012-January/067487.html
 
 
 Although, this other one suggests using the latter 40 ps of his MSD
 
 
 http://lists.gromacs.org/pipermail/gmx-users/2009-November/046990.html
 
 
 Your help is greatly appreciated.
 
 
 Thanks,
 
 
 Bernard
 
 
 
 
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-- 
Florian Dommert
Dipl. - Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: domm...@icp.uni-stuttgart.de
Homepage: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

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[gmx-users] g_msd and MSD analysis

[Mr Bernard Ramos]

Hi everyone!

I have a 20 ns  simulation (2fs timestep but coordinates saved every 0.2 ps)  
and I was able to calculate the mean-square-displacement of the oxygen atoms of 
my water solvent. The entire MSD plot looks very linear to me. I need to fit 
this set of MSD data to obtain the diffusion coefficient. However, I am not 
sure if I will have to use the entire MSD points or may be just to consider a 
few picoseconds at the latter part of the simulation time. In papers I have 
read, they use up to a 100 ps, although no mention were made as to where those 
set of points came from.  Please help.

This post seems to suggest a nanosecond window for the analysis of the MSD curve

http://lists.gromacs.org/pipermail/gmx-users/2012-January/067487.html

Although, this other one suggests using the latter 40 ps of his MSD

http://lists.gromacs.org/pipermail/gmx-users/2009-November/046990.html

Your help is greatly appreciated.

Thanks,

Bernard-- 
gmx-users mailing listgmx-users@gromacs.org
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