From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Jun 03 2011 - 07:05:47 CDT
try alpha { instead of alpha{
*
*
-ajasja
On Fri, Jun 3, 2011 at 13:21, 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
>
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