Re: Large number of simulations in parallel using replica exchange.

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Feb 11 2019 - 22:06:38 CST

Definitely something along those lines. Or pass environment variables to
the script using e.g. $env(SLURM_ARRAY_TASK_ID) if using Slurm.

Setting up charm++ partitions correctly takes a lot of work that may be too
much if you just want to run a bundle of uncoupled jobs.

Giacomo

On Mon, Feb 11, 2019, 10:46 PM Aravinda Munasinghe <aravinda1879_at_gmail.com
wrote:

> Hi,
> If you want only to change psf, pdb, output name and the parameter file,
> why not simply write a bash script to iteratively create all the inputs and
> execute 6000 simulations?.
> Best,
>
> On Mon, Feb 11, 2019 at 3:54 PM Dipak Balasaheb Sanap <dipakbs_at_udel.edu>
> wrote:
>
>> Hi, I have a simple problem. I need to run large number of short
>> simulations in parallel for different systems. And, my conf file has all
>> the parameters same except structure, coordinates, parameters and
>> outputname. I am planning to use replica exchange with no communication
>> among replicas so I can run all of the simulations in single command.
>> Something like this, namd2 replica.conf +replicas 6000 which uses just
>> exchanges variable parameters and run 6000 simulations in parallel. My
>> question is, how can I write replica.conf file to switch the parameters.
>> Below is my normal conf file for a single simulation and I have commented
>> where I need to switch the variable (variable 1,2,3 and 4). I am aware that
>> I need to use myReplica function or something like that. Thank you very
>> much.
>>
>> ##########################################################
>> #ADJUSTABLE PARAMETERS ##
>> #############################################################
>> # Variable 1 and 2, use different psf and pdb file for every replica
>> structure input/cg_20_22_psfgen.psf
>> coordinates input/cg_20_22_psfgen.pdb
>>
>> set temperature 310
>> #Variable 3, choose output directory for every replica
>> set outputname output/iteration1_0.6
>>
>> firsttimestep 0
>> #############################################################
>> ## SIMULATION PARAMETERS ##
>> #############################################################
>> # Input
>> paraTypeCharmm on
>> #Variable 4, change parameter file for every replica.
>> parameters input/from-aa_20_22_0.6.par
>>
>> temperature $temperature
>> # Force-Field Parameters
>> exclude 1-2
>> cutoff 30.0
>> switching on
>> switchdist 20.0
>> pairlistdist 100.0
>> hgroupcutoff 0
>> # Integrator Parameters
>> timestep 100.0
>> nonbondedFreq 1
>> stepspercycle 20
>> dielectric 20
>> # Constant Temperature Control
>> langevin on
>> langevinDamping 2.0
>> langevinTemp $temperature
>> langevinHydrogen off
>> # Output
>> outputName $outputname
>> restartfreq 400
>> dcdfreq 1000
>> xstFreq 400
>> outputEnergies 400
>> outputPressure 400
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>> # Minimization
>> minimize 2000
>> reinitvels $temperature
>> run 100000
>>
>>
>
> --
> Aravinda Munasinghe,
>
>

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