From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Sun Dec 17 2017 - 22:35:33 CST
Hello,
I ran into this problem when trying to apply rmsd constrain with
"translateReference off", tried to run it with 2.12 and the nightly
version and gives the same error.
rmsd.conf:
colvar {
name r1
width 0.1
rmsd {
atoms {
atomsFile input.pdb
atomsCol B
atomsColValue 1.0
translateReference off
}
refPositionsFile input.pdb # same as input
refPositionsCol B
refPositionsColValue 1.0
}
}
namd output:
colvars: Initializing a new collective variable.
colvars: # name = "r1"
colvars: Initializing a new "rmsd" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # scalable = on [default]
colvars: Initializing atom group "atoms".
colvars: # name = "" [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # atomsOfGroup = "" [default]
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "input.pdb"
colvars: # atomsCol = "B"
colvars: # atomsColValue = 1
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "atoms" defined, 6444 atoms initialized: total
mass = 38697.1, total charge = 0.
colvars: Error: keyword "translatereference" is not supported, or not
recognized in this context.
PS: In the namd user guide, under "Advanced usage of the rmsd
component", It mentions "disabling the application of optimal
roto-translations, which lets the RMSD component decribe the deviation
of atoms from fixed positions in the laboratory frame: this allows for
custom positional restraints within the Colvars module;" To implement
that, is it simply just turning rotateReference and translateReference off?
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