Re: Alpha P.M.F. with NAMD 2.8

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri Jun 03 2011 - 07:16:05 CDT

Dear Prathit, please insert a space between "alpha" and "{", otherwise
"alpha" can't be recognized.

Giacomo
 On Jun 3, 2011 1:21 PM, "Prathit Chatterjee" <pc20apr_at_yahoo.co.in> wrote:
> 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 - 05:24:02 CST