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
fax: (+1)-215-573-6233
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_<at>_gmail.com
web: http://www.cmm.upenn.edu/
---- ----
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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