Thank you David for providing the general protocol running in the MC
barostat. From the code I conclude that the new states in the Markov
chain are generated by displacing the molecules, rather than changing
the volume, and then rescale the potential associated with the move. If
I understand you correctly, the reference that I am after, and the one
you based your code on, is the (quite general) protocol for the MC
barostat outlined in Allen & Tildesley? If not, please provide the
relevant reference that I could cite.
Thanks Niel for weighing!
Best,
Filip
On 2017-11-14 20:18, David Cerutti wrote:
> I'm kind of the person who introduced the MC barostat into Amber, via the
> mdgx code. Jason Swails and Scott Legrand ported it into pmemd. The
> reference is a good one; there are also discussions about it in
> Computational Simulation of Liquids by Allen and Tildesley if I recall
> correctly.
>
> In order to better understand the MC barostat, it's useful to consider the
> case of an ideal gas, and how the barostat does indeed correctly reproduce
> the intended pressure / volume relationship despite the naïve perception
> that a volume move on an ideal gas would not produce a change in the
> potential energy of the particles (which is purely kinetic). It's all
> about the effect of the work term PdV and the probability of making the
> move (see Barostats.c, line 832), which includes the number of particles N
> and the log of the volume change, on the metropolis acceptance criterion.
> That's the detailed balance relationship and the means by which PV = ((( N
> ))) RT.
>
> Dave
>
>
> On Tue, Nov 14, 2017 at 1:17 PM, Niel Henriksen <shireham.gmail.com> wrote:
>
>> Hi Filip,
>>
>> I did not implement the MC barostat in AMBER, but this paper should provide
>> useful background:
>> https://doi.org/10.1016/j.cplett.2003.12.039
>>
>> The relevant AMBER code is
>> here: $AMBERHOME/AmberTools/src/sander/barostats.F90
>>
>> --Niel
>>
>> On Tue, Nov 14, 2017 at 3:09 AM, filip <filip.persson.bpc.lu.se> wrote:
>>
>>> Dear AMBER developers,
>>>
>>> I would like to see a reference for the Monte Carlo barostat implemented
>>> in AMBER 16 in order to understand exactly how it works. The manual is
>>> lacking in detail here and is not of very much help unfortunately.
>>>
>>> Best regards,
>>> Filip Persson
>>>
>>> PhD student
>>> Department of Biophysical Chemistry
>>> Lund University
>>> Sweden
>>>
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Wed Nov 15 2017 - 00:30:02 PST
