From: Robert Elder (rmelder_at_gmail.com)
Date: Fri Nov 09 2012 - 11:17:41 CST
As a follow-up to the discussion below, I have a question: is the energy
from the metadynamics history-dependent bias reported by NAMD under the
MISC header?
More specifically, I would like to perform replica-exchange metadynamics,
and I need to ensure that the full potential energy is used in the
Metropolis criterion. I already have the RE-metadynamics scheme
*functional* but need to ensure that it is *correct*. I've looked through
the NAMD source code and it seems that all the Colvar bias energies
(including metadynamics) are reported under MISC, but I am very new to the
code so any advice would be helpful.
Thanks to Aron Broom and Dr. Fiorin for the useful exchanges that have
allowed me to make it this far :)
-- Robert Elder PhD Student Department of Chemical and Biological Engineering University of Colorado-Boulder On Wed, Apr 4, 2012 at 6:32 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 > to). > > 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)? >> >> Thanks, >> >> ~Aron >> >> -- >> Aron Broom M.Sc >> PhD Student >> Department of Chemistry >> University of Waterloo >> >> >
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