Running multiple walker metadynamics replicas as a bundle

From: zeynab hosseini (
Date: Mon Oct 26 2020 - 07:33:11 CDT

Dear all,

I want to perform multiple walker/well-tempered (MWWT) metadynamics through
several replicas. I followed the example test under this link
creating the namd (.namd file) and collective variable (.in file)
configuration files for each replicas (e.g, rep1.namd, and
rep2.namd, and so on ). From NAMD user guide
I‚ÄĆ understood that there are two way to run MWWT metadynamics replicas, (1)
as a bundle (i.e. a single job in a cluster’s queueing system) or (2) as
fully independent runs (i.e. as separate jobs for the queueing system). I
think I‚ÄĆ know how to run the second one (please correct me if I'm wrong):

charmrun /usr/local/bin/namd2 ++local +p8 +replicas 2 test.rep1.namd >
charmrun /usr/local/bin/namd2 ++local +p8 +replicas 2 test.rep2.namd >

I‚ÄĆ tested the 2nd case and it worked. But I don't know how to perform the
first one. i.e. to run a single job and to get all replicas proceed
simultaneously. Would that be possible to guide me? (I assume that it is
related to the common.tcl provided in the example test
I don't know the proper commands to launch it).

All the best,

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