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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