Re: alpha pmf

From: JťrŰme Hťnin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri May 06 2011 - 07:58:37 CDT

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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