Alpha P.M.F. with NAMD 2.8

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 : Mon Dec 31 2012 - 23:20:22 CST