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

From: Yun Luo (luoyun724_at_gmail.com)
Date: Thu Sep 29 2011 - 14:25:57 CDT

I recompiled the new version on BG/P. It's working now. Thanks a lot!

Lyna

On Sep 29, 2011, at 10:11 AM, Chris Harrison wrote:

> 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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