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

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Thu Sep 29 2011 - 09:56:46 CDT

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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