Re: [AMBER-Developers] About ntt=2 in AMBER

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Sat, 1 Apr 2017 17:05:03 -0700

Well, I stand semi-corrected.

 From a purely mathematical point of view, Andersen indeed keeps the
correct NVT ensemble. It is basically a series of microcanonical
ensembles, which every time you apply the thermostat, switch total E
(and total momentum) in a markov-chain way and hence build a canonical
ensemble eventually.

In real life, extracting random forces and velocities according to a
Boltzmann distribution, which is what the proof of the correct NVT
ensemble requires, is not an easy thing to do for a finite system
running for a finite amount of time.

Also to keep in mind, Andersen destroys time continuity so diffusion
quantities are not correct. Also, reassigning momenta makes the system
memory very short, so barrier crossing rates can go down.

Adrian




On 4/1/17 2:21 PM, Jason Swails wrote:
> I thought it did...
>
> --
> Jason M. Swails
>
>> On Apr 1, 2017, at 5:02 PM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>>
>> Hi
>>
>> Technically, no, Andersen does not give you a true canonical ensemble.
>> However, you would have to look VERY closely at a simulation to figure
>> out that it is not.
>>
>> adrian
>>
>>
>>> On 4/1/17 12:04 PM, pengfei li wrote:
>>> Hi everyone,
>>>
>>> A quick question, will ntt=2 (the Andersen temperature coupling scheme) give a canonical ensemble? Thanks!
>>>
>>> Best regards,
>>> Pengfei
>>> _______________________________________________
>>> AMBER-Developers mailing list
>>> AMBER-Developers.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>> --
>> Dr. Adrian E. Roitberg
>> University of Florida Research Foundation Professor.
>> Department of Chemistry
>> University of Florida
>> roitberg.ufl.edu
>> 352-392-6972
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers

-- 
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Sat Apr 01 2017 - 17:30:02 PDT
Custom Search