Re: How to integrate multiple walkers 2D metadynamics results?

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Nov 07 2019 - 17:37:11 CST

Hi Canal, first of all try upgrading to the latest NAMD nightly build.
Thanks to Jim's help, I added extra checks that make the input/output
functionality more robust (the same checks are used when writing the NAMD
restart files):
https://github.com/Colvars/colvars/pull/276
There is also an important bugfix in the output of the PMF (the restart
files are fine):
https://github.com/Colvars/colvars/pull/259

About the exchange rate, on modern hardware optimal performance is around
few milliseconds/step, so 1000 steps is kind of short for a full cycle with
all replicas reading each others' files. Best to increase it by a factor
of 10 or more: I would have made its default value the same of the restart
frequency, but there is no telling how long that would be for each user's
input.

Regarding the PMFs, nothing special is needed. Each replica will write
PMFs with the same contents (the PMF extracted from the shared bias), so
they will be equal minus the fluctuations arising from synchronization.
You are probably confused by the partial output files, which are triggered
by dumpPartialFreeEnergyFile (a flag that is off by default).

Lastly, Gaussians 0.01 kcal/mol high added every 100 steps is quite a bit
of bias, and will be further multiplied by the number of replicas.

Giacomo

On Thu, Nov 7, 2019 at 6:06 PM Canal de Sebassen <
thecromicusproductions_at_gmail.com> wrote:

> 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
> }
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin

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