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

From: Chris Harrison (charris5_at_gmail.com)
Date: Thu Sep 29 2011 - 10:11:32 CDT

CVS version is now patched with the Alpha colvar bugfix. Should be
available in tomorrow's nightly build for those without CVS access.

Best,
Chris

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                          Voice: 773-570-0329 
http://www.ks.uiuc.edu/~char              Fax:   217-244-6078
Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr> writes:
> Date: Thu, 29 Sep 2011 16:56:46 +0200
> From: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
> To: JC Gumbart <gumbart_at_ks.uiuc.edu>
> Cc: Yun Luo <luoyun724_at_gmail.com>, namd-l_at_ks.uiuc.edu, Giacomo Fiorin
>  <giacomo.fiorin_at_temple.edu>
> Subject: Re: namd-l: ABF with Alpha colvar can't be used on supercomputer?
> 
> Sorry, you're right: the fix did not make it into 2.8, and still isn't
> in CVS either. We will send it in asap. Just in case, I am attaching a
> patch.
> 
> Lyna, you can forward this patch to the administrators of the
> supercomputer and politely ask them to apply and recompile? It is tiny
> and just a bugfix.
> 
> Cheers,
> Jerome
> 
> On 29 September 2011 15:05, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> > When was it fixed?  It still exists in the released 2.8.
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> > Of Jérôme Hénin
> > Sent: Thursday, September 29, 2011 5:05 AM
> > To: JC Gumbart
> > Cc: Yun Luo; namd-l_at_ks.uiuc.edu
> > Subject: Re: namd-l: ABF with Alpha colvar can't be used on supercomputer?
> >
> > Yes: a bug was introduced, that's what happened. Then it was fixed in
> > the next version.
> >
> > On 29 September 2011 08:05, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> >> 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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