I believe the factor 10/6 is involved here. The factor 1/6 comes from the fact that the diffusion formula has a factor of 1/2D, where D is the dimension (i.e. 3 in this case). So 1/(2*3)=1/6.
The factor of 10 is why you get 10e-5 instead of 10e-4 as you calculated.
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Vijay Manickam Achari [vjrajamany.yahoo.com]
Sent: Tuesday, August 06, 2013 10:33 PM
To: Amber mailing List
Subject: [AMBER] Diffusion constant's unit
Dear sir,
Greetings.
I need some clarification on determining the diffusion constant via ptraj.
It is stated in the diffusion output that:
DIFFUSION
Only the average results will be dumped to diffusion-malto-thermo63.dat_?.xmgr
The time between frames in psec is 5.000.
To calculated diffusion constants, calculate the slope of the lines(s)
and multiply by 10.0/6.0; this will give units of 1x10**-5 cm**2/s
The atoms in the calculation follow: :63
This meas if get the gradient value about 0.3 (for example), I should multiply this value (0.3) with 10/6 and I will get 0.5.
This value now can be written as 0.5 x 10e-5 cm^2/s.
Is that we multiply with 10 here to get the units fromangstrom^2/ps to cm^2/s ?
Because when I convert angstrom^2/ps to cm^2/s I get 10e-4 instead 10e-5 as given in the amber manual.
1 angstrom = 10e-8 cm
so 1 angstrom^2 = 10e-16 cm^2
1ps = 10e-12 s
so 1 angstrom / 1 ps
= 10e-16/10e-12
= 10e-4 cm^2/s
May I know how the 10e-5 cm^2/s as in the manual is obtained?
This verification may help a lot for me and others.
Many thanks in advance.
Regards
Vijay Manickam
Chemistry Department,
University of Malaya,
Malaysia
vjramana.gmail.com
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Received on Tue Aug 06 2013 - 22:30:02 PDT
