[gmx-users] g_msd

[Justin A. Lemkul]

minnale wrote:
>  
> Hi Users,
>     I have calculated lateral diffusion cofficient of POPC bilayer which 
> ran the simulation for 5ns.
> The command line is
> *g_msd -f 5ns_popc.xtc -s .tpr -o msd.xvg -lateral z
> 
> selected POPC system for calulation of msd
> at the end of the run showed like this
> 
> "Used 501 restart points spaced 10 ps over 5000 ps
> 
> Fitting from 500 to 4500 ps
> 
> D[      POPC] 0.0218 (+/- 0.0244) 1e-5 cm^2/s"
> 
> Could you please tell me
> 1. The input files I have given whether correct or not.

I don't know, are your files correct?

Usually one selects some reference atom for MSD calculations, like P8.  I don't 
know how whole molecules are treated, probably by center of mass.

> 2. The 'D' value which got is correct or not?

What does the literature tell you?

> 3.what's the experimental value?

Again - literature.  No one here is going to do your homework for you.

-Justin

> 
> Thanks in advance.
> 
> 
> 
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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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