From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Sun Nov 05 2017 - 10:17:13 CST
Hi Prapasiri, your overall understanding (1-6) is correct. The file-based
muliple-replicas infrastructure is designed to work as an extension of the
single-replica workflow, by adding the options replicaID and optionally
replicaRegistry.
Regarding your two questions:
1. The replicas will communicate through files, the paths of which are
maintained in the registry file. For this reason, you should run the
simulations on a fast file system, preferably not NFS (contact your
sysadmins to know what kind of shared filesystem is there between nodes).
2. The replicas *should* explore their own space, but this is a condition
that you have to check for (e.g. checking that each explores a different
energy basin).
If you want to run a quick test, you can try the example input files at:
https://github.com/Colvars/colvars/tree/master/namd/tests/library/011_multiple_walker_mtd
Giacomo
On Fri, Nov 3, 2017 at 7:30 PM, Prapasiri Pongprayoon <fsciprpo_at_ku.ac.th>
wrote:
> Hi All,
>
> I’m new to NAMD and need your valuable help. I ‘m now doing metadynamics
> of drug translocation through membrane protein. The simulations go well,
> but I suspect that it will require large CPU time for my drug to explore
> all configuration space. So, I decide to move to the multiple-replicas
> metadynamics. Based on the manual, it seems that I need to:
>
> 1. turn on “multipleReplicas”
> 2. Add replicaID, replicasRegistry, replicasUpdateFrequency, and
> dumpPartialFreeEnergyFile
>
> After going through the manual, I still don’t understand the process
> clearly. So, it would be very appreciated, if you could explain how to set
> up the run.
>
> From my understanding: (Pls correct me if it’s wrong)
> 1. To run multiple-replicas meta dynamics, I need a number of pdbs with
> different drug’s positions. Each system is called “replica” where each is
> defined as replicaID. 5 systems in their individual folder.
> 2. I still need to have a single file (put in replicasRegistry) containing
> the paths of “colvar.state" and “hill.traj” files that will be generated
> when all five start running.
> 3. If I have 5 systems = 5 replicas (everything is the same except
> position of drug in each system), I need to run them separately with its
> own .conf and colvar files. The only difference among them are “replicaID”.
> Is this correct?
> 4. When all are run, they will talk to each other via “colvar.state" and
> “hill.traj” files defined in “replicasRegistry”. The file just has lines
> showing the location of state and hill files.
> 5. 5 runs will generate their own outputs and .pmf, but the pmf obtained
> from each replica is generated by combining data among 5 replicas. So, 5
> pmfs from 5 replicas are generated, but there are the same. Is this
> correct? For the partial.pmf, does this file reflect the influence of
> individual run on the overall pmf file?
> 6. To restart the runs, I just add “colvarsInput input.colvars.state" in
> .conf of all five.
>
> These are what I understand from the manual and NAMD list.
>
> If these are correct, I still have some questions
> 1. If I have 5 replicas, I have to run 5 replicas independently. How do
> they communicate if they don’t start running at the same time?
> 2. Based on the recipe above, does it mean that each replica explores its
> own configuration space and then the data obtained from each replica will
> be combined and used to get the overall pmf?
>
> Is there any tutorial for multiple-replicas metadynamics that I can go
> through?
>
> Thanks for your help and patience in advance.
>
> Regards,
> Prapasiri
>
>
-- Giacomo Fiorin Associate Professor of Research, Temple University, Philadelphia, PA Contractor, National Institutes of Health, Bethesda, MD http://goo.gl/Q3TBQU https://github.com/giacomofiorin
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