From: Prathit Chatterjee (pc20apr_at_yahoo.co.in)
Date: Thu May 05 2011 - 01:21:02 CDT
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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