Re: Umbrella Sampling after multiple replicas metadynamics

From: Aron Broom (
Date: Fri Sep 28 2012 - 16:53:09 CDT

ok perfect, thanks for the rapid response!


On Fri, Sep 28, 2012 at 5:33 PM, Giacomo Fiorin <>wrote:

> Hi Aron, no, the files are how they are supposed to be: each replica
> stores its own stuff, and all energies and gradients are summed together at
> runtime. For that you must continue to run with multiple replicas, if you
> continue a single one by decoupling it from the others it's just not the
> same simulation any more.
> So yes, you can make a single-replica state file to continue from a
> certain point, by summing together the data in those files just like you
> suggested.
> Giacomo
> On Fri, Sep 28, 2012 at 5:23 PM, Aron Broom <> wrote:
>> 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
>> replicas?
>> Thanks,
>> ~Aron
>> --
>> 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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