Thanks David for the clarification! I think this irons out the kinks in
my understanding about the MC barostat in AMBER for now. I use pmemd so
the distinction in behaviour between the routines is important. I notice
now that the MC barostat is actually described in the AMBER 16 manual on
page 514, but in the mdgx chapter rather than sander (which I only
looked at). In the next revision of the manual I think it would be
helpful for the users if the mdgx section is referenced in connection
with the the sander section about the barostats.
Thanks for introducing the MC barostat to AMBER!
/Filip
On 2017-11-15 09:27, David Cerutti wrote:
> That's correct about the reference--however, the new states ARE generated
> by rescaling the volume. The box dimensions change, and the centers of
> mass of each molecule move along with it. mdgx and pmemd work differently
> in this respect--pmemd rescales centers of mass and thereafter treats every
> molecule as a rigid body, but mdgx treats all molecules as stretchable
> along with the box, insofar as the molecules themselves are flexible, again
> to my recollection. The particle count is different in each case--mdgx
> counts all rigid molecules (i.e. waters), all rigidly constraints groups
> (i.e. SHAKE-constrained bonds), and all other atoms in the system when it
> tallies up N. pmemd looks solely at the number of separate molecules, to
> go hand-in-hand with its molecular virial convention.
>
> Dave
>
>
> On Wed, Nov 15, 2017 at 3:13 AM, filip <filip.persson.bpc.lu.se> wrote:
>
>> 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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Received on Wed Nov 15 2017 - 02:00:03 PST
