# Re: [AMBER] Distance diffusion calculation in ptraj and cpptraj

From: Huang Jing <jing.huang8911.gmail.com>
Date: Tue, 27 Dec 2016 15:04:07 +0200

Hello,
I am still a beginner of amber ; the unit of MSD would be Angstrom^2 ;
in my opinion, no scaling factor is for mean square displacement and "2n
n=3" is needed for the calculation of diffusion coefficient; the calculated
diffusion coefficient is the "sug_O[Slope]/2n" n=3,
Perhaps my answer is not all correct and you need to examine them,as I am
still a beginner,
I followed up the official amber tutorial :

jing

Dr. Jing Huang
*Institute of Chemistry and the Lise Meitner-Minerva Center for
Computational Quantum*
*Chemistry, Hebrew University of Jerusalem, Givat Ram Campus, Jerusalem
91904, Israel*

On Tue, Dec 27, 2016 at 9:58 AM, wei <lwstudy.sina.com> wrote:

> Dear all,
> I want to calculate distance diffusion coefficient D for a sugar molecule
> in bulk water. I have tried ptraj and cpptraj analysis tools to realize
> this calculation respectively.
> After running the ptraj script, I got five output files (diff.dat_x.xmgr,
> diff.dat_y.xmgr, diff.dat_z.xmgr, diff.dat_r.xmgr, diff.dat_a.xmgr). Let me
> display few lines of data deposited in diff.dat_r.xmgr:
> 3990.000 1990.5193992.000 2023.4453994.000 1913.1503996.000
> 1941.7723998.000 1964.5964000.000 1982.162
> 1. What does the second column represent and what are their unit? It seems
> that the second column lists MSD values, but have it been scaled by a
> factor (for instance, 2n, n=3 in the case of r)?
> Let me also paste the calculated D-values by cpptraj:
> #Set sug_O[D] sug_O[Slope] sug_O[Intercept] sug_O[Corr]
> sug_O[Label] 1 0.3546 0.2128 521.8718
> 0.7209 sug_O_AvgDr 2 0.4605 0.0921 -145.4334
> 0.6208 sug_O_AvgDx 3 0.3895 0.0779 492.8230
> 0.5437 sug_O_AvgDy 4 0.2138 0.0428
> 174.4822 0.5268 sug_O_AvgDz
> 2. I was wondering what is the unit of the calculated D values on the
> second column?
> Regards,Liu Wei
>
>
>
> --------------------------------
>
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Received on Tue Dec 27 2016 - 05:30:02 PST
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