From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Sat May 07 2011 - 00:33:28 CDT
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: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
To: Prathit Chatterjee <pc20apr_at_yahoo.co.in>
Cc: Giacomo Fiorin <giacomo.fiorin_at_gmail.com>; Ajasja Ljubetič <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: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>; Ajasja Ljubetič
> <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: Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>
> To: Ajasja Ljubetič <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 Ljubetič <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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