Re: alpha pmf

From: felmerino_at_uchile.cl
Date: Wed May 04 2011 - 02:37:06 CDT

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 100colvarsRestartFrequency 2analysis 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 typeabf { 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 : Wed Feb 29 2012 - 05:23:53 CST