problem restarting multiple walker metadynamics

From: Amy Rice (
Date: Wed Mar 11 2015 - 14:59:46 CDT

Hi all,
I am running multiple walker/well tempered metadynamics; I have 28 walkers
and would ultimately like to run for 15ns each. Due to walltime
limitations, I have to restart the simulation after 7.5ns, which is where
the problem is occurring. After inspecting the pmfs generated after
restarting, it seems to me that the colvar state information from before
the restart is not being included, and that a new pmf is being generated
instead. However, the log file shows that the colvars.state file is being

colvars: Collective variables biases initialized, 1 in total.
colvars: Restarting from file "01/meta.KR12.colvars.state".
colvars: Restarting collective variable "alpha" from value: 0.050172
colvars: Collective variables module initialized.

Here is the relevant region of one of the restart configuration files:
structure KR12.ionized.psf
coordinates KR12.ionized.pdb
bincoordinates 01/meta.KR12.coor
extendedsystem 01/meta.KR12.xsc
binvelocities 01/meta.KR12.vel


colvars on
colvarsInput 01/meta.KR12

and one of the colvar configuration files:
colvarsTrajFrequency 5000

colvar {
        name alpha
        width 0.005

        lowerboundary 0.0
        upperboundary 1.0

        lowerwallconstant 10
        upperwallconstant 10

        alpha {
                residueRange 19-28
                psfSegID P1

metadynamics {
        colvars alpha
        hillWeight 0.5
        newHillFrequency 100
        hillwidth 2.5066
        wellTempered on
        biasTemperature 3000
        saveFreeEnergyFile on
        writeHillsTrajectory on
        multipleReplicas on
        ReplicaID 1
        replicaUpdatefrequency 1000
        dumpPartialFreeEnergyFile on

Here is the final pmf generated before the restart (after 7.5ns):

The first three pmfs generated post-restart, same scale:
(red is after 0.1ns of the restarted run, green is 0.2ns, and blue is 0.3ns)

Last pmf generated before the restart (pink/purple) and the first two after
restarting (red and green):

As I said, it seems to me that the information from before the restart is
not being included. Is there a different way to restart multiple walker
metadynamics runs, or perhaps an option that I neglected to include in my
configuration files?
Thank you for your help!

Amy Rice
Ph.D. Student
Physics Department
Illinois Institute of Technology

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