Hi Jason,
Thank you for the reply, I'm feeling a lot more comfortable now about the Monte Carlo barostat.
Quick question however: I've noticed that a lot of the long time scale simulations done by the Shaw group use NPT for their production ensemble, however the AMBER aMD paper (LCT Pierce et al.) was able to sample similar space using the dihedral/total energy boosts in the canonical NVT ensemble. I'm wondering if I could also use the NVT ensemble for aMD simulations where I expect a large structural change or if I should try out NPT.
Thanks again,
Parker
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Friday, July 25, 2014 1:20 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Berendsen vs. Monte Carlo
> On Jul 24, 2014, at 10:14 PM, Parker de Waal <Parker.deWaal.vai.org> wrote:
>
> Hi Everyone,
>
> I haven't been able to find any literature, besides the manual, describing the implementation of the Monte Carlo barostat in AMBER14 and was wondering if someone could provide some insight.
It is described in the Allen and tildesley book. There is a brief description in the amber 14 manual (check the mdgx chapter as well, there might be more information there as well).
You can also look at the code (barostats.F90). It's actually a remarkably simple algorithm, so you may find the code enlightening.
>
> Currently I'm trying to sample the energy landscape of an apo protein using aMD that I suspect is very unstable, due to the geometry of the ligand binding pocket, and suspect will undergo a large significant change. Because of this I would like to use the NPT ensemble during my production MD instead of NVT to allow a greater range in energy fluctuation. If possible I would like to use ntb =2, ntp =1, barostat = 2 to save computer time and speed along the process, however I'm concerned that the Monte Carlo barostat won't be as effective as the Berendsen implementation to achieve this goal.
It's possible that it may take a while for the MC barostat to find an effective step size. But it is actually a more rigorously correct barostat. And quite a bit faster for pmemd.cuda.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jul 25 2014 - 05:30:02 PDT
