Re: [AMBER] how to calculate scattering trajectory

From: Adrian Roitberg <>
Date: Sun, 20 Mar 2011 22:09:47 +0100

Well, without changing the code, if you have a restart file with
velocity information, you 'could' hack it to change the velocity of the
cis-pinonic acid to whatever you want. Now, you want to do this in a way
that the total angular momentum is zero (or something else you want) and
you need to then run at constant energy, without a thermostat.

That should do it.

On 3/20/11 10:06 PM, Bill Ross wrote:
>> 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.
> I have never heard of Amber having the ability to assign a specified
> initial velocity to a component of the system. I think you may have to
> modify the code if you want this behavior.
> Bill
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                            Dr. Adrian E. Roitberg
                              Associate Professor
                Quantum Theory Project, Department of Chemistry
                            University of Florida
on Sabbatical in Barcelona until August 2011.
AMBER mailing list
Received on Sun Mar 20 2011 - 14:30:03 PDT
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