Running multiple walker metadynamics replicas as a bundle

From: zeynab hosseini (hosseinizeynab93_at_gmail.com)
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
<https://github.com/Colvars/colvars/tree/master/namd/tests/library/011_multiple_walker_mtd>,
creating the namd (.namd file) and collective variable (.in file)
configuration files for each replicas (e.g, rep1.namd, rep1.in and
rep2.namd, rep2.in and so on ). From NAMD user guide
<https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html#sec:colvarbias_meta_mr>
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 >
test.rep1.log
charmrun /usr/local/bin/namd2 ++local +p8 +replicas 2 test.rep2.namd >
test.rep2.log

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
<https://github.com/Colvars/colvars/blob/master/namd/tests/library/011_multiple_walker_mtd/common.tcl>
but
I don't know the proper commands to launch it).

All the best,
Zeynab

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