Re: alpha pmf

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: J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr>; Ajasja Ljubetińć <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: J√©r√īme H√©nin <jhenin_at_ifr88.cnrs-mrs.fr> >To: Ajasja Ljubetińć <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 Ljubetińć <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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