Re: [AMBER] how to calculate scattering trajectory

From: Wen Xu <>
Date: Mon, 21 Mar 2011 10:11:41 -0500

Hi Adrian,
   I did as what you suggest. First I got the restart file after
equilibrating the system
at Temp=298.15 for 10ps. Then I manually changed the cis-pinonic acid
in the restart file to 185m/s (about 0.1 angstrom 1/20 ps). Then I ran
the molecular
dynamics at NVE ensemble. However then temperature of the system goes
up from
298.15 K to 352 K after 50 ps. I know without a thermostat the
temperature will
not stay.
However, in reality. The spherical water cluster is in a bath gas of
Nitrogen under 1
atmospheric pressure. The cis-pinonic acid concentration is on the
order of ppb level.
I think the kinetic energy of the system should dissipate quickly by
colliding with the
bath gas (nitrogen). Therefore, I think that including a thermostat
will be more
appropriate. My question is can I use the NVT ensemble to study the
scattering trajectory?
But using NVT ensemble, I should be able to get the temperature of the
system constant.
Thank you for your help.

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

On Sun, 20 Mar 2011 22:09:47 +0100
  Adrian Roitberg <> wrote:
> Well, without changing the code, if you have a restart file with
> velocity information, you 'could' hack it to change the velocity of
> cis-pinonic acid to whatever you want. Now, you want to do this in a
> that the total angular momentum is zero (or something else you want)
> 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
>>> 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
>> modify the code if you want this behavior.
>> Bill
>> _______________________________________________
>> AMBER mailing list
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
> on Sabbatical in Barcelona until August 2011.
> Email
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Received on Mon Mar 21 2011 - 08:30:05 PDT
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