Date: Mon Aug 16 2010 - 12:06:24 CDT
I have a question regarding the colvars function of NAMD.
I am trying to run a simulation of a small molecule in a
membrane channel. I would like to enforce a positional
restraint on the small molecule to constrain it at a certain
position along the channel axis (z-axis) for initial
equilibration. I found a NAMD tutorial that did a similar
thing by confining an ion within a sphere of a given radius
(In Silico alchemy: A tutorial for alchemical free-energy
perturbation calculations with NAMD) using the colvars module.
I therefore tried to follow a similar protocol, but I wanted
to be sure that I’m thinking about this and setting up my
ColvarsConfig in the right way.
Here is my ColvarsConfig…
axis (0.0, 0.0, 1.0)
Here, my “main” atomsfile includes all the atoms of my small
molecule and my “ref” atomsfile contains atoms of 6 protein
residues of the membrane channel. What I am hoping that this
script does is to apply a harmonic potential on the COM of the
small molecule using a force constant of 100 kcal/mol to
restrain it within 10 angstroms (5 angstroms above and 5
angstroms below) of the COM of the 6 protein residues along
Could you please let me know if I am on the right track and
applying this script in the right way?
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