Hi,
The diffusion constants in 'diffout <file>' have been converted to
1E-5 cm^2/s. The conversion factor is provided in case one wants to do
the fit some other way. The manual should be more clear about that.
Sorry for the confusion.
-Dan
On Wed, Mar 11, 2020 at 2:20 PM Chetna Tyagi <cheta231.gmail.com> wrote:
>
> Dear Amber users,
>
> I am completely confused by which units are used to report the diffusion
> coefficient results.
>
> #Set WAT_O[D] WAT_O[Slope] WAT_O[Intercept] WAT_O[Corr]
> WAT_O[Label]
> 1 5.7387 3.4432 -1806.9110 0.9999
> WAT_O_AvgDr
> 2 8.7133 1.7427 -1379.2619 0.9999
> WAT_O_AvgDx
> 3 8.4717 1.6943 -656.5336 0.9998
> WAT_O_AvgDy
> 4 0.0311 0.0062 228.8845 0.9952
> WAT_O_AvgDz
>
> Here the second column is diffusion coefficient. Is it in Å2 ps–1
> or already converted to cm2 s–1
>
> The mean square displacement is surely calculated in Å2 ps–1
>
> But then it writes "To convert from units of Å 2 /ps to 1x10 -5 cm 2 /s,
> the slope is multiplied by 10.0/(2n)". So which is it?
>
> Please help.
> --
> Best wishes
> Chetna
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 12 2020 - 11:00:02 PDT
