From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Apr 16 2018 - 14:08:06 CDT
Hi Dhiraj,
Why are there three "atoms" declarations inside the spinAngle? Admittedly I haven't looked into the source to see if this is legal syntax, but I don't think that it is.
-Josh
On 2018-04-16 12:34:27-06:00 owner-namd-l_at_ks.uiuc.edu wrote:
Hi
I am trying to use the spinAngle colvar and using the moving frame of reference. however namd is showing error that
"colvars: Error: keyword "refpositionsfile" is not supported, or not recognized in this context."
how should I solve this problem?
thank you
Dhiraj
my colvar script is
colvar {
name spin
outputAppliedForce on
spinAngle {
atoms {
atomsFile spin.pdb
atomsCol B
atomsColValue 1
refPositionsFile spin.pdb
refPositionsCol B
refPositionsColValue 1
axis (-0.47851067781448364, 0.23966480791568756, 0.8447416424751282)
}
atoms {
CenterReference on
RotateReference on
refPositionsFile spin.pdb
refPositionsCol B
refPositionsColValue 1
}
atoms {
psfSegID AP1
atomNameResidueRange CA 212-220
centerReference yes
rotateReference yes
fittingGroup {
psfSegID AP1
atomNameResidueRange CA 1-211
}
refPositionsFile spin.pdb
}
}
}
harmonic {
name harm
colvars spin
forceConstant 16200
centers 0
targetCenters -90
targetNumSteps 10000000
}
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:21:00 CST