Re: multiple replicas metadynamics

From: Mihaela Drenscko (
Date: Mon Jan 09 2017 - 16:02:45 CST

I am using namd/2.11. I hope this version works.
Still, something is not clear to me.
it says that all all replicas pmf will be combined in one, but it doesn't
say how it is accomplished. So I suppose all 10 replicas I am working with
must have the same outputName, say r? (Initially I gave output names as 1,
2 3 ... 10, but then I didn't have one pmf file in the end - I had 10
different pmf files, with names 1 2..10.).
Another thing is how to distinguish from pmf and partial pmf, if they have
the same name:
When multipleReplicas is on, the file *outputName*.pmf contains the
combined PMF from all replicas, provided that useGrids is on (default).
Enabling this option produces an additional file *outputName*.partial.pmf,
which can be useful to quickly monitor the contribution of each replica to
the PMF.

So if outputName.pmf is the name of the combined file, then
outputName.partial.pmf is whose replica pmf? The naming and indexing of
these files is not clear.

So the problem is, if I give different names to my 10 replicas, then I get
10 sets of pmf files, such as 1.10000.pmf, 2.10000,pmf, ... 10.10000.pmf
and the files are not combined, because the code doesn not know what is the
name of the combined file.

On the the other hand, if I give the same name (as r) to each of the 10
replicas outputs, then I get one pmf fiole output, but for the partial pmf
output, there is no way to knaow to which replicas it belongs, as all
replicas outputs have the same name.

Please let me know if there is something I didn't realize from the MRM

Thank you,

On Fri, Jan 6, 2017 at 9:24 PM, Mihaela Drenscko <>

> Hi,
> When I run namd with multiple replicas metadynamics, I don't get files
> and,
> where outputwq is the name of each outputName. Instead, the paths of these
> file are written in a file called metadynamics1.outputwq.files, text:
> /.colvars.metadynamics1.1.state
> /.colvars.metadynamics1.1.hills
> These files should read outputwq.metadynamics1.1.state and
> outputwq.metadynamics1.1.hills, according to:
> html#sec:colvarbias_meta
> So these files can't be read by other replicas and pmfs can't be combine
> into one. All i get are partila pmf, from each replica.
> Any suggestions, what is wrong? Why .state and .hills files are not
> written with outputName prefixes, without the need foe their paths to be
> written in afile?
> Thank you,
> Mihaela

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