[gmx-users] g_msd ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 
> Hi
> 
> # g_msd_mpi is part of G R O M A C S:
> #
> # Giant Rising Ordinary Mutants for A Clerical Setup
> #
> @    title "Diffusion Coefficients / Molecule"
> @    xaxis  label "Molecule"
> @    yaxis  label "D"
> @TYPE xy
>          0    0.907803
>          1      3.5355
>          2     4.34231
>          3     3.83589
> 
> 
> xaxis = Molecule # from .top file
> yaxis = diffusion coefficient
> 
> 1. what does the first row represent ? ( Molecule # = 0   ??? )

Indexing starts from zero, probably.

> 2. what is the unit for the diffusion coefficient ??

g_msd should have printed an average value of D, complete with units.

> 3. why are the diffusion coefficients quite different for the same type 
> of molecules ( water ) ??

Probably due to poor statistics.  Individual diffusion coefficients are usually 
less interesting than averaged behavior.

-Justin

> 
> 
> Thank you
> Lin
> 
> 
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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