Re: ABF with Alpha colvar can't be used on supercomputer?

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Sep 29 2011 - 01:05:53 CDT

Something changed between NAMD versions 2.8b2 and 2.8b3 that causes this error, although I can't figure out what it is. Hopefully Jerome can enlighten us?

On Sep 28, 2011, at 3:38 PM, Yun Luo wrote:

>
> Dear NAMD developers,
>
> I want to use ABF with colvar "alpha" for a ten-alanine peptide. It seems work when I tested my script on linux cluster. But when I use NAMD2.8 on Blue Gene/P supercomputer, the output gives error message as below:
> colvars: ----------------------------------------------------------------------
> colvars: Initializing a new collective variable.
> colvars: # name = alpha
> colvars: Initializing a new "alpha" component.
> colvars: # componentCoeff = 1 [default]
> colvars: # componentExp = 1 [default]
> colvars: # period = 0 [default]
> colvars: # wrapAround = 0 [default]
> colvars: # psfSegID = HLX
> 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.
> FATAL ERROR: Error in the collective variables module: exiting.
> -----------------------------------------------------------------------------------------
>
> Is this a bug related to supercomputer version?
> My colvar and abf input file is shown as below:
> colvarsTrajFrequency 100
> colvarsRestartFrequency 100
>
> colvar {
> name alpha
> width 0.1
> lowerboundary 0.0
> upperboundary 1.0
> lowerwallconstant 10.0
> upperwallconstant 10.0
> extendedLagrangian on
>
> alpha {
> residuerange 1-10
> psfSegID HLX
> hbondcoeff 0.5
> angleref 88
> angletol 15
> hbondcutoff 3.3
> hbondexpnumer 6
> hbondexpdenom 8
> }
> }
>
> abf {
> colvars alpha
> fullSamples 10000
> applyBias yes
> outputFreq 100
> hideJacobian no
> }
>
> Thanks !
>
> Lyna

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