From: Nicolas Floquet (nicolas.floquet_at_univ-montp1.fr)
Date: Mon Aug 25 2014 - 09:40:06 CDT
Hello all !
i'm trying to use a vector (eigen vector) as the reaction coordinate for
a metadynamics.
here's my colvar file :
colvarsTrajFrequency 10000
colvar {
name r1
lowerBoundary -5.0
lowerWallConstant 50.0
upperBoundary 5.0
upperWallConstant 50.0
width 0.05
outputVelocity off
outputAppliedForce off
eigenvector {
atoms {atomNumbersRange 1-2} # I PUT HERE ONLY TWO ATOMS FOR TESTING
refPositionsFile ./test.pdb # CONTAINS THE TWO ATOMS subjected to the
vecotr IN THE PDB FORMAT
vector -0.00088 0.00061 0.00092 -0.00105 0.00063 0.00098 # THE 3N
COMPONENTS OF THE EIGEN VECTOR
}
}
metadynamics {
name metadyn_r
colvars r1
usegrids on
hillWeight 0.01 # Default is 0.01 - higher numbers = faster
dumpFreeEnergyFile yes
newHillFrequency 100 # Default is 100 - lower numbers = faster
}
Please help me, the error message is :
colvars: Initializing a new collective variable.
colvars: # name = r1
colvars: Initializing a new "eigenvector" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: Initializing atom group "atoms".
colvars: Atom group "atoms" defined, 2 initialized: total mass =
13.019.
colvars: # refPositions = [default]
colvars: # refPositionsFile = ./test.pdb
colvars: # refPositionsCol = "" [default]
colvars: # vector =
colvars: Using vector components from input file.
colvars: Error: vector components do not match the number of
requested atoms.
colvars: If this error message is unclear, try recompiling with
-DCOLVARS_DEBUG.
FATAL ERROR: Error in the collective variables module: exiting.
Thank you in advance for your help.
Nicolas
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