Yes you would but....
the velocity of the cis-pinonic acid acid will then be modified by the
thermostat ! (the velocity direction would also probably be changed,
depending on the thermostat also). Hence, what you think as "velocity'
for your particle will change even before hitting the water shell.
I would need to think carefully about this, but other than having a
thermostat attached just to the water, I do not see a way. Attaching a
thermostat to just a part of the system requires code changes.
Adrian
On 3/21/11 4:11 PM, Wen Xu wrote:
> 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
> velocity
> 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<roitberg.qtp.ufl.edu> wrote:
>> 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.
>> Email roitberg.ufl.edu
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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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.
Email roitberg.ufl.edu
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Received on Mon Mar 21 2011 - 08:30:06 PDT
