From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Fri Jun 03 2011 - 06:21:46 CDT
Dear Sir,
sorry to disturb you again. The 2.8 Version of NAMD has been out and as suggested by you earlier, I tried again to start my alpha p.m.f. calculation with this new NAMD version. Please have a look of my input file format below -
colvarsTrajFrequency 100
colvarsRestartFrequency 2
analysis off
###########################
colvar {
############################################
name helix
width 0.1 ##given this value so that it comprises with the lower and upper boundary
lowerBoundary 0.0
upperBoundary 1.0
outputValue on
alpha{
residueRange 71-82
psfSegID ASYN
hBondCoeff 0.5
angleRef 88
angleTol 15
hBondCutoff 3.3
hBondExpNumer 6
hBondExpDenom 8
}
}
#############################################
# Bias type
metadynamics {
colvars helix
hillWeight 0.01 #height of each hills in kcal/mol
newHillFrequency 100
hillWidth 1.253 #[(square root of 2pi)/2]
useGrids on
gridsUpdateFrequency 100
dumpFreeEnergyFile on
writeHillsTrajectory on
}
The error which shows now says that -
colvars: # name = helix
colvars: Error: no valid components were provided for this collective variable.
But, I have seen from the NAMD user guide that I have provided the variables essential for the pmf calculation.
Please help me in this regard.Any suggestion from other expertise will also be very helpful.
Thanks and Regards
Prathit Chatterjee
03.06.2011
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