Re: alpha pmf

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed May 04 2011 - 03:04:14 CDT

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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