From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Sep 28 2012 - 16:23:15 CDT
I'm not sure anyone has tried this, but I suspect someone who works on the
collective variables modules might have some input.
Something I've done before which was very successful, was to use
metadynamics to get a rough estimate of the Free energy surface, and then,
restart the simulation, but with the hill height changed to 0 and a
harmonic bias in order to do umbrella sampling. The value of this is that
the umbrella sampling with WHAM can act to smooth out any lingering errors
in the metadynamics and also provide a reliable estimate of the error.
The above works great for a single metadynamics run. I've recently done
some multiple replicas metadynamics in NAMD 2.9, and I would like to repeat
this kind of process. I thought that because the replicas communicate, the
final *.state file for the last replica to finish would essentially have
all the data, and I could just use that to restart. It seems that isn't
the case, and each replica's state file only holds the energies in it's
grids for the biases it specifically applies? This seems at odds with how
multiple replicas simulations run, but when I restart from one of these
state files, I don't get back to what the final *.pmf looked like, and
appear to only be getting a small portion.
Is there a way to merge all these state files together? For instance,
could I simply take the columns of the state file that correspond to the
grid energies and just add all those values together, and hope that the
resulting state file is what I'm looking for? And would one do that for
both the energies and the gradients?
I suppose this also applies to any time one might want to change the number
of replicas being used after a restart?
Or maybe I've just done something horribly wrong, and the final *.state
file from any run really is the combination off all the hills for all the
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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