Hi,
On Tue, Dec 27, 2016 at 2:58 AM, wei <lwstudy.sina.com> wrote:
> 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)?
All values output by ptraj are overall mean square displacements
(Ang^2) except for the '_a.xmgr' files, which contains total distance
traveled in Ang. I don't think there's any scaling factor applied.
> 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?
Diffusion constants output from cpptraj are given in units of 1x10^-5
cm^2/s (I think/hope this is mentioned in cpptraj output/Amber16
manual).
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Dec 28 2016 - 10:00:03 PST
