How to integrate multiple walkers 2D metadynamics results?

From: Canal de Sebassen (thecromicusproductions_at_gmail.com)
Date: Thu Nov 07 2019 - 17:04:15 CST

Hello,

Say I run a metadynamics simulation with 10 walkers. I then get 10
different pmf files. If my simulation was in 2D, how do I get a single
energy landscape? Do I use abf_integrate?

Also, what are some good practices when running these kind of simulations?
I haven't found many examples. This is one my current colvars files. I plan
to get about 1-5 microseconds of data. Is a replicaUpdateFrequency of 1000
too large? I tried with a smaller one but I get problems because some files
of a replica cannot be found by another one (maybe due to lagging?).

Thanks,

Sebastian

colvarsTrajFrequency 100

colvar {

    name d1

    outputAppliedForce on
    width 0.5

    lowerBoundary 0.0
    upperBoundary 30.0

    upperWallConstant 100.0

    distanceZ {
forceNoPBC yes
        main {
            atomsFile labels.pdb
atomsCol B
atomsColValue 1.0
        }
        ref {
            atomsFile labels.pdb
atomsCol B
atomsColValue 2.0
        }
    }
}

colvar {

    name d2

    outputAppliedForce on
    width 1

    lowerBoundary 0.0
    upperBoundary 10.0

    upperWallConstant 100.0

    coordNum {
cutoff 4.0

        group1 {
            atomsFile labels.pdb
atomsCol O
atomsColValue 1.0
        }
        group2 {
            atomsFile labels.pdb
atomsCol B
atomsColValue 2.0
        }
    }
}

metadynamics {
    colvars d1 d2

    useGrids on
hillWeight 0.01
    newHillFrequency 100
dumpFreeEnergyFile on
dumpPartialFreeEnergyFile on
saveFreeEnergyFile on
writeHillsTrajectory on

    multipleReplicas yes
    replicaID rep1
    replicasRegistry replicas.registry.txt
    replicaUpdateFrequency 1000
}

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2019 - 23:21:00 CST