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
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:18 CST