Applying a positional restraint with colvars module

From: bkziervogel_at_uchicago.edu
Date: Mon Aug 16 2010 - 12:06:24 CDT

Hi,

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…

colvarsTrajFrequency 100
colvarsRestartFrequency 100

colvar {
    name colvar1

    width 0.1

    lowerboundary -15.0
    upperboundary 15.0

    lowerWall -5.0
    upperWall 5.0

    lowerWallConstant 100.0
    upperWallConstant 100.0

    distanceZ {
        main {
           atomsFile amp_main.ref
             atomsCol B
             atomsColValue 1.0
         }
         ref {
                atomsFile ref.ref
                atomsCol B
                atomsColValue 1.0
         }
          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
the z-axis.

Could you please let me know if I am on the right track and
applying this script in the right way?

Thank you!!

Brigitte

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:09 CST