Re: error in the orientationAngle

From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Sun May 22 2011 - 05:01:55 CDT

Dear Giacomo, Thanks for your previous reply. When I am using metadynamics instead of abf, I am changing the last portion of my colvars-input file as follows - Instead of# Bias type abf { colvars tilt fullSamples 100 hideJacobian no outputFreq 100 applyBias yes } I am supplying te varibales of metadynamics as - # Bias type meta { colvars tilt 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 message now shown is - colvars: Collective variables initialized, 1 in total. colvars: Collective variables biases initialized, 0 in total. colvars: Error: keyword "meta" is not supported, or not recognized in this context. I shall be very grateful if further advice/suggestions is shared with. With regards Prathit Chatterjee ________________________________ From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com> To: Prathit Chatterjee <pc20apr_at_yahoo.co.in> Cc: NAMD Mailing list <namd-l_at_ks.uiuc.edu> Sent: Saturday, 21 May 2011 8:17 PM Subject: Re: namd-l: error in the orientationAngle Prathit: as the error message says, and as specified in the manual already, you can't use ABF on orientationAngle. Giacomo On Sat, May 21, 2011 at 4:51 AM, Prathit Chatterjee <pc20apr_at_yahoo.co.in> wrote: 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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