From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Fri May 06 2011 - 05:54:55 CDT
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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