[AMBER] Distance diffusion calculation in ptraj and cpptraj

From: wei <lwstudy.sina.com>
Date: Tue, 27 Dec 2016 15:58:46 +0800

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?
Thanks in advance!
Regards,Liu Wei


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Received on Tue Dec 27 2016 - 00:00:02 PST
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