From: Jeff Wereszczynski (jmweresz_at_mccammon.ucsd.edu)
Date: Thu Oct 25 2012 - 13:17:27 CDT
Hi NAMD List,
I have another question about using multiple walker/well tempered
metadynamics in NAMD. Briefly, here is the metadynamics portion of my
colvars file:
---------------------------------------------------------------------------------------------
colvarsRestartFrequency 250000
...
metadynamics {
name metad
colvars colvar1 colvar2
hillWeight .3
hillWidth 10
newHillFrequency 100
replicaUpdateFrequency 1000
wellTempered on
biasTemperature 1600
multipleReplicas on
replicaID 00
replicasRegistry
/scratch/scratchdirs/jmweresz/srta/meta_1600/repfile
dumpFreeEnergyFile on
usegrids on
saveFreeEnergyFile on
dumpPartialFreeEnergyFile on
}
---------------------------------------------------------------------------------------------
I have a total of 21 replicas running, which all have identical colvar
files except for the "replicaID" field. I have been running simulations in
5 ns increments and I have each of the replicas running at the same time.
So I have all 21 replicas running from 0-5 ns using their own "input1.inp"
files, waiting at the 5 ns point for any slow replicas to catch up (a short
wait), and then running from 5-10 ns with "input2.inp" files. I also set
the colvarsRestartFrequency to only write restart files and PMFs every 500
ps.
Everything proceeds normally for the first 5 ns, but my issue shows up when
I start the second input file. From what I can tell, when input2.inp
starts up for each replica, it reads the colvars.state file properly for
that replica, but it does not read the colvars.state files for the other
replicas. The result of this is that for the time between when I start up
that second input file and when it hits a "colvars restart" interval,
sampling in each replica contains hills from the initial run of that
replica but not from the other replicas. As the simulation proceeds, hills
from the other replicas are added, but the full sampling history of the
other replicas are not added until I hit a colvars restart interval.
If that is confusing, maybe this example makes more sense. With each
input file going for 5 ns, and a colvarrestart frequency of 500 ps, an
individual replica sees hills from previous sampling times likes this:
Time Hills from this replica Hills from other replica
5 ns 0-5 ns 0-5 ns
5.5 ns 0-5.5 ns *5-5.5
ns*
6 ns 0-6 ns 0-6 ns
This problem is quite clear when I look at the PMFs at time 5.5 ns, as the
PMFs should be nearly identical between replicas, but they are not. In
fact, they mostly look like the "partial" PMFs (since that is where most of
their sampling comes from). At 6 ns though, the PMF files look nearly
identical between replicas.
Overall this creates a convergence problem, as there is a chunk of time in
which metadynamics is not properly sampling the underlying PMF. One way to
minimize this is to reduce colvarsRestartFrequency to a small value (say
500) so that only a few hills are added on the incorrect metadynamics
landscape, but this isn't ideal as then I get a very large number of PMF
files and I'm wasting some time unnecessarily writing restart and PMF
files. So this seems like a bug to me, but perhaps there's something I'm
doing wrong?
Also, while I have your ear, I wanted to make sure that the PMFs are being
properly computed. Looking in the colvarbias_meta.C file, I can see on
line 1512-1517 how the scaling factor for the well tempered algorithm is
being applied to the single replica case by defining the multiply_constant
variable to -1*(DT+T)/T if well tempered is used and -1 if it isn't, but it
looks to me that in the multiple replica case that it is only ever set to
-1 (line 1539), which would mean that the scaling factor is not being
applied in this case. Of course, I could be reading this file wrong and
there could be a correction elsewhere, so I just wanted to check on this.
Thanks for your help!
-- Jeff Wereszczynski Postdoctoral Scholar University of California, San Diego http://mccammon.ucsd.edu/~jwereszc
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