Re: alpha pmf

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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