Re: Free energy of conformational change

From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
Date: Wed May 20 2009 - 11:22:38 CDT

Hello Branko, do you need an example configuration for a free energy
profile using as a collective variable the distance between two
groups? In that case, you may take the one I sent in reply to a
similar question a few weeks ago about metadynamics (which shares a
lot of the code with ABF in NAMD 2.7b1):

colvar {

   name d

   lowerBoundary 0.0
   upperBoundary 10.0
   width 0.2

   distance {
       group1 { atomNumbers 1 }
       group2 { atomNumbers 2 }
   }
}

metadynamics {
   colvars d
   dumpFreeEnergyFile yes
}

I'm not sure if this is what you want: if you're already familiar with
ABF or need it for a specific reason, replace the keyword
"metadynamics" with "abf" :-P

Please note also that the choice of the collective variable type (a
distance, a torsional angle, a RMSD, etc.) can affect the results.
This is why you have several ones in NAMD 2.7b1.

Giacomo

---- ----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
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---- ----

On Wed, May 20, 2009 at 7:15 AM, Branko <bdrakuli_at_chem.bg.ac.yu> wrote:
> Hallo Chris,
>
> I am note the respond to Lixia, so I need something similar - to obtain
> (only) the free energy of conformational change on small (flexible)
> molecules in two explicit solvents. Using ABF on ver. 2.6 and defining
> distance between two groups of atoms in studied molecule works without
> problem, but using colvar on 2.7b1 (which offer plenty of possibility) looks
> something more complicated. So, please if some example of configuration file
> is available, let me know. 2.7b1 ug give more than sufficient information,
> but I have no experiences with making of input (configuration) for such
> calculations. Likely that all atoms in molecule can be used for free energy
> of conformational change evaluation.
> Thanks in advance
>
> Branko
>
>
>

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