From: Haohao Fu (fhh2626_at_gmail.com)
Date: Sun Dec 17 2017 - 23:54:10 CST
It should be "centerReference".
Best,
Haohao
2017-12-18 12:35 GMT+08:00 Victor Kwan <vkwan8_at_uwo.ca>:
> 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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