Using harmonic walls on water molecules

From: Moises Ernesto Romero (moiseser_at_uci.edu)
Date: Mon Feb 04 2019 - 19:14:39 CST

Hi All,

I am trying to confine a large amount of water molecules within an annulus
of a protein which is in a vacuum.
The water molecules escape along the z-directions.
I have tried to accomplish this by defining harmonic walls using the
collective variables modules.
My first attempt involved defining all waters as a single collective
variable:
colvarsTrajFrequency 100

colvar {
        name water
        lowerboundary -39.0
        upperboundary 48.0
        lowerWallConstant 5.0
        lowerWall -38.0
        upperWall 47.0
        upperWallConstant 5.0
distanceZ {
                main { atomNumbersRange 179209-224829 }
                ref { atomNumbersRange 224830-316341 }
                axis { (0.0 , 0.0 , 1.0) }
}
}
The waters still escaped.
My second attempt involved selecting each of the ~15,000 waters as an
individual collective variable; however, this will take a long time to
initialize the simulation.
What is smarter way to go about this? Thanks!

-- 
Moises Romero
PhD Student
Andricioaei Group
UC Irvine

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