Umbrella sampling with hbond

From: Payne, Christy (Christy.Payne_at_nrel.gov)
Date: Thu Mar 22 2012 - 19:05:24 CDT

I am attempting to setup a set of umbrella sampling simulations using the hbond colvar; however, I get an error with the acceptor selection in my colvar configuration file ( Error: in parsing "acceptor"). I have copied my colvar configuration file below. There doesn't appear to be a problem with the donor selection, as I have moved it before the acceptor selection without issue. I would greatly appreciate any suggestions as to what I may be doing incorrectly here.

Thanks in advance!
Christy

colvarsTrajFrequency 100
analysis on

colvar {
    name catres

# Estimate of the typical fluctuation amplitude for this collective variable
    width 0.01

# RC values between 0 and 1
    lowerboundary 0
    upperboundary 1

# Values at which to start applying biasing potential
    lowerWall 0.01
    upperWall 0.99

# Bias potential force constants
    lowerWallConstant 2.5
    upperWallConstant 2.5

# Output the applied force in the .traj file
    outputAppliedForce on

# Reaction coordinate (or collective variable to be used)
# Here it is hbond which goes from an nondimensional value of 0 to 1

    hbond {

# Acceptor is glycosidic oxygen
        acceptor {
           atomNumbers 5658
         }

# Donor is OD2 of D221
        donor {
           atomNumbers 2035
         }

# These are the default values for hbond
        cutoff 3.3
        expNumer 6
        expDenom 8
    }
}

# Application of harmonic potential
harmonic {
    name umbsamp
    colvars catres
    centers 0.5
    forceConstant 2.5
}

histogram {
    colvars catres
    outputFreq 100
}

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