stfcdiffusion will work like the traditional diffusion command when com is not used. So this is only an additional option (the other one being that you can compute diffusion in a region defined by mask2 and lower and upper limits). Which one to choose is really a question of what you want to learn. Same goes for b).
Cheers,
Hannes.
________________________________________
From: Vijay Achari [glycoamber.gmail.com]
Sent: 13 February 2015 06:11
To: AMBER Mailing List
Subject: [AMBER] Water diffusion - in 2D and 3D
Dear experts,
I have two questions to ask.
a) I tried to calculate water diffusion in hydrated bilayer system using
two commands from ambertools14, *diffusion* and
*stfcdiffusion.*
I understand the *diffusion* command does calculate the average of movement
of every atoms in a molecules frame-wise. While the *stfcdiffusion* command
calculate the diffusion of center of mass (COM) of molecule's atoms in a
system
I wish to know which method is more appropriate to use in a reasonable way?
b) In a hydrated lipid bilayer system, do we calcualte the water diffusion
in 2D (x-y) or 3D (x-y-z)?
Thank you.
Vijay
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Received on Fri Feb 13 2015 - 00:30:02 PST
