[AMBER] how to calculate scattering trajectory

From: Wen Xu <wxu.mail.chem.tamu.edu>
Date: Sun, 20 Mar 2011 14:51:01 -0500

Dear All Amber Users,
    I have a question related to the calculation of scattering
trajectory. My system
is an isolated water sphere of diameter 6nm plus a isolated
cis-pinonic acid (a kind
of dicarboxylic acid). The initial distance between the cis-pinonic
acid and the center
of the water sphere is 20 nm. I want to give the cis-pinonic acid an
initial velocity
towards the center of the water sphere. The magnitude of the initial
velocity equals
the maxwell-boltzmann distribution average velocity. With this initial
velocity and
configuration, I will do the scattering calculation to study the
trajectory of cis-pinonic
acid after impinging on the water droplet surface. This process is
very similar to the
paper by Du. et al. 2009. J. Am. Chem. Soc., 2009, 131 (41), pp
But in their paper, they didn't show how to set the initial velocity
of the ClO. Therefore, I
don't know how to set the initial velocity of the cis-pinoninc acid in
my calculation.
I know maybe this is trivial. However, I looked the amber manual I
tried very hard, but I
still can not find it.
So, Could some one tell me how to set the magnitude of the initial
velocity as the maxwell
boltzmann average value and constrain the initial velocity in certain
direction? Thanks in

Wen Xu
Graduate Research Assistant
Chemistry Department
Texas A&M University, College Station

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Received on Sun Mar 20 2011 - 13:00:03 PDT
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