Re: where do I find info about freeEnergy ?

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Tue Jun 08 2010 - 15:36:49 CDT

Hi Leonardo,

The free energy module you are talking about is now deprecated. It has
been replaced with the collective variables (colvars) module. See the
section "Collective variable calculations" in the user's guide for
full documentation.

In your case, you would have to define a distance between the two
atoms, and the harmonic restraint. The colvars configuration file
would read like this:

colvar {
      name myDistance
      distance {
            group1 { atomNumbers 24 }
            group2 { atomNumbers 42 }
       }
}

harmonic {
       colvars myDistance
       centers 42.0
       forceConstant 42.0
}

That's assuming you want an average distance of 42 ångströms between
atoms 24 and 42 (PDB numbering), with a force constant of 42
kcal/mol/Å^2.

Cheers,
Jerome

On 8 June 2010 20:28, Leonardo Herrera <ldhz04_at_yahoo.com.mx> wrote:
> Hi
> I need to find some information about freeEnergy topic and comand urestraint. Can somedody help me to find this? or Give me an example?
> All this to make an harmonic restraint betwen two atoms.
> Thanks a lot.
>
> MenB Leonardo David Herrera Zúñiga     POSGRADO EN QUÍMICA  UAMI Biofisicoquímica  Universidad Autonoma Metropolitana IztapalapaTel. +52 (55) 5804 4674    ldhz04_at_yahoo.com.mx

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