On 12/5/16 8:56 AM, Jason Swails wrote:
> On Mon, Dec 5, 2016 at 7:46 AM, Fabrício Bracht <fabracht1.gmail.com> wrote:
>
>> Hi. The first part of the question is regarding ntcnstph and ntrelax
>> variables. Since the ntrelax value controls the solvent relaxation period
>> after a state change, should the ntcnstph times the number of titratable
>> residues be larger than the ntrelax value?
>>
Hi,
Just to be clear, Jason wanted to write "
Note that in EXPLICIT solvent, *every* titratable residue attempts to
"
> Note that in implicit solvent, *every* titratable residue attempts to
> change its protonation state (independently in random order) every ntcnstph
> steps. Note that this is very different than implicit solvent, where only
> a single residue is attempted every ntcnstph steps. The reason for this is
> primarily one of computational performance, but the arguments in the manual
> explaining how to pick ntcnstph based on the number of residues you're
> titrating does not apply in explicit solvent.
>
> ntrelax should be chosen to ensure reasonable solvent relaxation (the
> longer the better) and reasonable computational performance (the shorter
> the better). My original paper walks through this choice.
>
>
>
>> Also I was wondering if there is some sort of consensus for good (wouldn't
>> even ask for optimal) values of nstlim and numexchg for replica exchange
>> constant ph simulations in explicit solvent.
>>
> I like using 100 for both ntcnstph and nstlim (numexchg should be chosen
> based on how long of a simulation you want to run). Replica exchange
> attempts are *virtually* cost-free, although synchronization imposes more
> overhead in explicit CpHMD simulations than any other simulation (due to
> replicas having different numbers of relaxation steps to execute and the
> ones with fewer having to wait for the replicas with more relaxation to
> finish).
>
>
>
>> I mean, how many protonation state exchanges have to be made within an
>> nstlim window?
>>
> They are independent sampling processes, so there are no restrictions.
>
> I would recommend consulting the paper introducing the method, as it
> addresses several of these questions directly.
>
> HTH,
> Jason
>
--
Dr. Adrian E. Roitberg
University of Florida Research Foundation Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Dec 05 2016 - 08:30:02 PST
