[gmx-users] g_msd additional information

Justin Lemkul jalemkul at vt.edu
Wed Dec 12 13:39:09 CET 2012

On 12/12/12 4:37 AM, dakoenig wrote:
> Dear GROMACS Experts,
> I am using GROMACS to simulate the self-diffusion coefficient of a wide
> range of pure systems (e.g. alkanes).
> Unfortunately the information given in the manual regarding g_msd and its
> exact calculation in GROMACS is insufficient for me.
> Does somebody got some idea of papers/additional information/books for this
> topic?
> I am especially interested in the calculation of the error bar.

This post will probably be helpful:


If you need more information, you'll have to be more specific about what you 
need to know.  This topic isn't something about which one will find lots of 
dedicated reference material; it really boils down to a single equation.  Aside 
from normal I/O routines, the rest of the code does the statistical analysis 
(above).  Of course, all the information you need to know is in the code ;)



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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