Re: alpha pmf

From: JťrŰme Hťnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue May 10 2011 - 03:37:24 CDT

Prathit,

I tried to run your input. I get this error message:
Error: keyword "lower" is not supported, or not recognized in this context.

that happens because you wrote "lower boundary" instead of one word
"lowerBoundary"

If I correct this, I get the expected error:
Error: one or more of the components of colvar "hlx_frac" does not
support system force calculation.

If you are running these tests on a supercomputer, I suspect that the
input file accessible to the compute nodes is not updated correctly,
and that you are actually running an outdated input file.

Jerome

On 10 May 2011 09:18, Prathit Chatterjee <pc20apr_at_yahoo.co.in> wrote:
> Dear Giacomo,
>           I have tried again just now and the same error message is given to
> me. I ma attaching my respective input and output files along with the
> submit script. Please have a look.
> Regards
> Prathit
>
> ________________________________
> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> To: Prathit Chatterjee <pc20apr_at_yahoo.co.in>
> Cc: J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr>; Ajasja Ljubetińć
> <ajasja.ljubetic_at_gmail.com>; "felmerino_at_uchile.cl" <felmerino_at_uchile.cl>;
> NAMD Mailing list <namd-l_at_ks.uiuc.edu>
> Sent: Tuesday, 10 May 2011 2:35 AM
> Subject: Re: namd-l: alpha pmf
>
> Hello Prathit: are you really sure that is the error message corresponding
> to the file you posted, after removing atomsFile and the related options?
> After trying your input on NAMD 2.8, it looks to me like you didn't remove
> them.
>
> This is the error message that you should get with your input, once you fix
> it as I said:
> colvars:   Error: one or more of the components of colvar "hlx_frac" does
> not support system force calculation.
> (which means that the colvar "hlx_frac" has been enabled correctly, but ABF
> can't be used with it unless you enable extendedLagrangian).
>
> My suggestion is: first change the configuration file by removing atomsFile
> and the related options (i.e. what I asked you already).  Once you have
> followed this suggestion, and get into a new and different error condition,
> only then you can ask for more help.
>
> Giacomo
>
> ---- ----
>   Giacomo Fiorin - Postdoctoral Researcher
>   ICMS - Institute for Computational Molecular Science - Temple University
>   1900 N 12 th Street, Philadelphia, PA 19122
>   giacomo.fiorin_at_temple.edu
> ---- ----
>
>
>
> 2011/5/7 Prathit Chatterjee <pc20apr_at_yahoo.co.in>
>
> Dear Jerome,
>           I had meant that it gives me the same error message as previous.
>
> It is -
> 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.
>
> Thanks and regards
> Prathit
> ________________________________
> From: J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr>
> To: Prathit Chatterjee <pc20apr_at_yahoo.co.in>
> Cc: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>; Ajasja Ljubetińć
> <ajasja.ljubetic_at_gmail.com>; "felmerino_at_uchile.cl" <felmerino_at_uchile.cl>;
> NAMD Mailing list <namd-l_at_ks.uiuc.edu>
> Sent: Friday, 6 May 2011 6:28 PM
> Subject: Re: namd-l: alpha pmf
>
> Sorry, "it does not work" contains no useful information.
>
> Jerome
>
> On 6 May 2011 12:54, Prathit Chatterjee <pc20apr_at_yahoo.co.in> wrote:
>> Sir,
>>     I have even tried by opting out the options like "atomsfile, atomscol,
>> atomscolValue" . But it does not work.
>> Prathit
>> ________________________________
>> From: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>> To: Prathit Chatterjee <pc20apr_at_yahoo.co.in>
>> Cc: J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr>; Ajasja Ljubetińć
>> <ajasja.ljubetic_at_gmail.com>; "felmerino_at_uchile.cl" <felmerino_at_uchile.cl>;
>> NAMD Mailing list <namd-l_at_ks.uiuc.edu>
>> Sent: Thursday, 5 May 2011 8:01 PM
>> Subject: Re: namd-l: alpha pmf
>>
>> Hello, Prahit: "atomsFile" and the related options/keywords are not part
>> of
>> the "alpha" component.  Have you tried removing them?
>>
>> Giacomo
>>
>> ---- ----
>>   Giacomo Fiorin - Postdoctoral Researcher
>>   ICMS - Institute for Computational Molecular Science - Temple University
>>   1900 N 12 th Street, Philadelphia, PA 19122
>>   giacomo.fiorin_at_temple.edu
>> ---- ----
>>
>>
>>
>> On Thu, May 5, 2011 at 2:21 AM, Prathit Chatterjee <pc20apr_at_yahoo.co.in>
>> wrote:
>>
>> Respected Dignitaries,
>>                    Thanks a lot for your kind suggestions. Anyways, I
>> shall
>> be trying to implement the meta-dynamics tools to calculate the alpha pmf.
>> But I shall be also waiting patiently for the response of Dr. Jerome
>> regarding the bug issue.
>>
>> Thanks in advance
>> Prathit Chatterjee
>>
>> ________________________________
>> From: J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr>
>> To: Ajasja Ljubetińć <ajasja.ljubetic_at_gmail.com>
>> Cc: "felmerino_at_uchile.cl" <felmerino_at_uchile.cl>; pc20apr_at_yahoo.co.in; NAMD
>> Mailing list <namd-l_at_ks.uiuc.edu>
>> Sent: Wednesday, 4 May 2011 2:47 PM
>> Subject: Re: namd-l: alpha pmf
>>
>> Hi Prathit,
>>
>> I completely second the comments from Felipe and Ajasja.
>>
>> On top of that, you have probably found a bug. We'll try and have a
>> look at it asap (which may not be right away, unfortunately).
>>
>> Best,
>> Jerome
>>
>> On 4 May 2011 10:04, Ajasja Ljubetińć <ajasja.ljubetic_at_gmail.com> wrote:
>>> Hi,
>>> Perhaps you could try to turn on extendedLagrangian formalism, which
>>> enables
>>> you to use any colvar in an ABF simulation.
>>> A word of warning: this is still considered a bit experimental.
>>> Regards,
>>> Ajasja
>>>
>>> On Wed, May 4, 2011 at 09:37, felmerino_at_uchile.cl <felmerino_at_uchile.cl>
>>> wrote:
>>>>
>>>> Hey,
>>>>
>>>> To be able to perform an ABF simulation namd has to know the force on
>>>> the
>>>> collective variable. To the best of my knowledge (take a look at the
>>>> user
>>>> guide) the alpha component is not compatible with ABF (for the reason
>>>> mentioned above). Myabe you should try metadynamics.
>>>>
>>>> best
>>>>
>>>> Felipe
>>>>
>>>> ----Mensaje original----
>>>> De: pc20apr_at_yahoo.co.in
>>>> Fecha: 04-may-2011 1:55
>>>> Para: "NAMD Mailing list"<namd-l_at_ks.uiuc.edu>
>>>> Asunto: namd-l: alpha pmf
>>>>
>>>> Dear NAMD Experts,
>>>>                        I am trying to find out the potentials of mean
>>>> force with respect to the helicity fraction of a portion of the protein
>>>> through ABF. The colvar config file is listed below -
>>>>
>>>> #Global options:
>>>> colvarsTrajFrequency    100
>>>> colvarsRestartFrequency 2
>>>> analysis                off
>>>> ###########################
>>>> colvar {
>>>>         ############################################
>>>>         name                    hlx_frac
>>>>         width                   1.0
>>>>         lower boundary          0.0
>>>>         upper boundary          1.0
>>>>         outputValue             on
>>>>         outputVelocity          off
>>>>         outputSystemForce       off
>>>>         outputAppliedForce      off
>>>>         extendedLagrangian      off
>>>>
>>>>         alpha {
>>>>                 residueRange    71-82
>>>>                 psfSegID        ASYN
>>>>                 hBondCoeff      0.5
>>>>                 angleRef        88
>>>>                 angleTol        15
>>>>                 hBondCutoff     3.3
>>>>                 hBondExpNumer   6
>>>>                 hBondExpDenom   8
>>>>                 atomsFile       hlx_frac.pdb
>>>>                 atomsCol        O
>>>>                 atomsColValue   2.0
>>>>         }
>>>>
>>>> }
>>>> #############################################
>>>> # Bias type
>>>> abf {
>>>>         colvars         hlx_frac
>>>>         fullSamples     100
>>>>         hideJacobian    no
>>>>         outputFreq      100
>>>>         applyBias       yes
>>>> }
>>>> ######################################
>>>>
>>>>
>>>> The error message which is coming in the output file is -
>>>>
>>>> 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.
>>>>
>>>> Any kind of suggestion or correction will be highly appreciated.
>>>>
>>>> Thanks and regards
>>>>
>>>> Prathit Chatterjee
>>>>
>>>>
>>>
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