From: Amy Rice (arice3_at_hawk.iit.edu)
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
read:
colvars:
----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars:
----------------------------------------------------------------------
colvars: Restarting from file "01/meta.KR12.colvars.state".
colvars: Restarting collective variable "alpha" from value: 0.050172
colvars:
----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars:
----------------------------------------------------------------------
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
colvars on
colvarsConfig alpha01.in
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
replicasRegistry
/oasis/scratch/arice3/temp_project/first/registry
replicaUpdatefrequency 1000
dumpPartialFreeEnergyFile on
-------------------------------------------------------------------------------------
Here is the final pmf generated before the restart (after 7.5ns):
https://drive.google.com/file/d/0B2-4_f9dh-l2cllJa2QxaDZzQWc/view?usp=sharing
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)
https://drive.google.com/file/d/0B2-4_f9dh-l2NzljbVZITzdlQ0U/view?usp=sharing
Last pmf generated before the restart (pink/purple) and the first two after
restarting (red and green):
https://drive.google.com/file/d/0B2-4_f9dh-l2b3VDTDhDQ0Jsdjg/view?usp=sharing
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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