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: 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 >> >> > >

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