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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:13 CST