RE: Umbrella Sampling input parameters

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Jul 10 2018 - 05:40:51 CDT

Hi Jun,

There are two ways of setting up umbrella sampling with colvars. The most common approach is to use an initial SMD pull to cover your reaction coordinate space (center = initial value, targetCenter = final value), and then pick frames from that pull to seed your umbrellas. In that case, each umbrella would have a center, with no defined targetCenter (since the umbrella isn't moving). The other alternative combines your SMD and umbrella sampling together, and sequentially moves umbrellas. In this case, you would use the targetNumStages parameter to move your umbrellas sequentially along your chosen reaction coordinate. This has two drawbacks: 1.) You can't easily make your simulations longer if you are not converged, since the same trajectory is used for all states. 2.) Your umbrella sampling calculation becomes serial, as each window depends on the result of the last one. Since oftentimes umbrella sampling has like a microsecond of MD behind it, this would take prohibitively long for real systems. So if it were me, I'd use the more common approach.

Another piece of advice is to just set your width to 1 unless you are combining dissimilar collective variables together. The applied force constant is unrelated to the upper or lowerboundary parameters. It is instead determined by the forceconstant parameter applied to the harmonic and the width of the collective variable, as described in the documentation of the forceconstant parameter. This also clarifies that you indeed should NOT set upper/lower limits. This is effectively already done by the harmonic potentials, and adding extra biases will skew WHAM analysis.

-Josh

Example umbrella sampling configuration file:

#############################################################
## Collective Variables ##
#############################################################
# Global parameters
colvarsTrajFrequency 50
colvarsTrajAppend off
analysis off
colvar {
        name contactcount
#Here I don't follow my own advice and set the width to be not 1. This was so that the whole reaction coordinate could be mapped to the range (0,1)
        width 977.429
        coordNum {
                expNumer 2
                expDenom 24
                cutoff 10.0
                group1 {
                        atomsFile beta.pdb
                        atomsCol B
                        atomsColValue 1
                }
                group2 {
                        atomsFile beta.pdb
                        atomsCol B
                        atomsColValue 2
                }
        }
}
harmonic {
    name contactpull
    colvars contactcount
    centers 684.20000973
#Technically, I didn't need to specify targetCenters, since the default is for targetCenters=centers
    targetCenters 684.200010
    forceConstant 2000.000000
    targetNumSteps 100
}

On 2018-07-10 01:00:28-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

Hi all,
I want to implement Umbrella Sampling and questions about input parameters.
My colvars is a distance between two molecules.
If my initial distance is 11, and I want to make free energy profile along the distance in range of from 2 to 30 with width of 0.1.
Then what should be my "centers" and "targetCenters"?
If I set "centers" to 11 and "targetCenters" to 31, then will I not be able to explore the region between 2 and 11?
And will the force constant be [upperboundary - lowerboundary]*width^2 ?
I heard that I should not define lower/upperBoundary, or lower/uppderWallConstant for Umbrella Sampling, is it correct?
Thank you
Jun

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