From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Fri Jun 03 2011 - 07:55:52 CDT
Dear Sir
Thank you for the correction. But, after the correction, I get the same error message as I had mentioned you earlier when I was using NAMD_2.8b1. In the last portion of the output file it states -
colvars: Initializing a new "alpha" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # psfSegID = ASYN
colvars: # hBondCoeff = 0.5
colvars: # hBondCutoff = 3.3
colvars: # hBondExpNumer = 6
colvars: # hBondExpDenom = 8
colvars: Error: cannot add atoms to a dummy group.
colvars: If this error message is unclear, try recompiling with -DCOLVARS_DEBUG.
I could not compile the NAMD as suggested by you earlier as I know not how to compile it. So, I was waiting for the 2.8 version and hoping that the error will not be shown once I use NAMD_2.8.
Regards
Prathit
________________________________
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: Friday, 3 June 2011 5:46 PM
Subject: namd-l: Re: Alpha P.M.F. with NAMD 2.8
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
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