Re: alpha pmf

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed May 04 2011 - 04:17:16 CDT

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 Ljubetiè <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
>>
>>
>
>

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:12 CST