Re: Umbrella Sampling input parameters

From: Junwoong Yoon (junwoony_at_andrew.cmu.edu)
Date: Thu Jul 12 2018 - 17:45:19 CDT

Hi Josh,

Thank you so much for your explanation. It was very helpful to prepare my
umbrella sampling strategy.
But I still have couple questions that bother me.

1) For SMD prior to umbrella sampling, can I use SMDDir 0 0 -1 if I am
trying to pull a molecule down along the z-direction?
Or should I still need to define a normalized direction between fixed atoms
and SMD atoms for SMDDir?
How will this be different if I'm calculating distance in x-y plane? For
example, pulling two molecules on a surface while their heights(z-dir
value) are fixed?

2) To make sure neighboring windows to overlap, what forceConstant should I
use if my width is 0.1, and each window is equally spaced by 1A?
    I used 0.025 based on the tutorial, but I want to clarify how does
0.025 scaled forceConstant allow windows to overlap.

My colvars file looks like,

colvar {
    width 0.1
    distance Z { }

    harmonic {
        centers $CENTER
        forceConstant 0.025

Thank you
- Jun

On Tue, Jul 10, 2018 at 6:40 AM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:

> 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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