Re: Running multiple walker metadynamics replicas as a bundle

From: zeynab hosseini (
Date: Wed Oct 28 2020 - 04:02:35 CDT

Hi Josh,

Thank you for your guidance..

All the best,

On Mon, Oct 26, 2020 at 12:04 PM Josh Vermaas <>

> Hi Zeynab,
> If you wanted two different simulations to execute independently within
> the queuing system, I don't think you'd use the +replicas options at
> all. +replicas 2 means that NAMD will run the .namd file twice under the
> same process (so that if one crashes, the whole simulation goes down).
> Based on the links you pointed to, +replicas 2 would write the same set of
> files. The trick to setting up multiple replicas under the same process is
> to use "myReplica" within the NAMD configuration file (
> to say what replica you are, and use that to setup the output files
> accordingly.
> -Josh
> On Mon, Oct 26, 2020 at 6:39 AM zeynab hosseini <
>> wrote:
>> 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 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 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 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
>> <> but
>> I don't know the proper commands to launch it).
>> All the best,
>> Zeynab

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