From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Apr 04 2012 - 20:24:56 CDT
Thank you for the reply, I look forward to testing this out. As to (2),
that is absolutely correct, I have no real theoretical basis for suggesting
it is possible, I just got carried away in the excitement concerning
replicas and metadynamics.
On Wed, Apr 4, 2012 at 8:32 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>wrote:
> Hello Aron, yes to (1), but since this is new code, so keep checking that
> the contents of the PMF files across all replicas are the same (or close
> About (2), I'm not even aware there is a formalism to handle more than one
> level of replica-parallelism at once.
> Anyway, temperature-exchange should be possible, for as long as you
> include the metadynamics energy in the Metropolis criterion. Likewise,
> bias-exchange is also possible by swapping the state files.
> On Wed, Apr 4, 2012 at 9:54 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>> I had two questions concerning metadynamics in NAMD 2.9b2, the first
>> quite specific to 2.9b2, and the other perhaps is more general and could
>> relate to 2.8 also.
>> 1) In 2.8 multiple replicas (multiple walkers) metadynamics was not
>> possible while useGrids was enabled, but I see the particular note
>> concerning this has been removed from the 2.9b2 user guide. It does,
>> however, say that a *.hills file is used for each replica as a kind of
>> communication buffer, which perhaps suggest that the hills still need to be
>> recorded analytically? Anyway, I'm wondering if it is possible now to do
>> multiple walkers/replicas for metadynamics while also having the benefit of
>> the grids.
>> 2) Is it possible (has anyone done this in NAMD?) to use the temperature
>> replica exchange Tcl script to perform Replica-Exchange metadynamics? I
>> don't see why it would be different in form from any other
>> temperature-based replica exchange method, but as I'm no expert in these
>> things I could easily be missing something. Moreover, the section on
>> temperature replica exchange claims that the scripts are in spirit easily
>> adapted for exchange based on things other than temperature. Is it
>> therefore possible to perform bias-exchange metadynamics? Could one even
>> combine both of those in order to do nested replica exchange for different
>> parameters (temperature and bias for instance)?
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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