[gmx-users] g_msd additional information

[Justin Lemkul]

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:

http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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