From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Sat May 21 2011 - 03:51:10 CDT
Dear NAMD Experts,
I tried to run a pmf calculation with abf as a function of orientation angle of the backbone of protein. I am pasting my input variables below -
###########################
colvar {
############################################
name tilt
width 1.0
lowerBoundary 0.0
upperBoundary 180.0
outputValue on
outputVelocity off
outputSystemForce off
outputAppliedForce on
extendedLagrangian off
#############################################
orientationAngle {
atoms {
atomNumbers 381
atomNumbersRange 1-93953
}
refPositionsFile protein_nat_bb.pdb
refPositionsCol O
refPositionsColValue 2.0
closestToQuaternion (1.0, 0.0, 0.0, 0.0) #quadruplet,the closer to (1,0,0,0) is chosen
}
}
#########################
# Bias type
abf {
colvars tilt
fullSamples 100
hideJacobian no
outputFreq 100
applyBias yes
}
######################################
I am also attaching the output file which is showing the details of acceptance of the variables of my colvars-input file but finally defining error in the colvars.
Any suggestions/advice will be deeply appreciated.
Thanks and regards
Prathit Chatterjee
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