Re: collective variables

From: Giacomo Fiorin (
Date: Wed Jun 17 2009 - 13:26:44 CDT

Hi Jarrod, such a restraint is relatively simple to set, but you have to
combine several features together. You'd have to define a distance variable
along the z axis, and force it to the value you want.

colvar {
  name d
  outputAppliedForce yes
  outputSystemForce yes
  distanceZ {
    axis (0.0, 0.0, 1.0)
    main { atomNumbers ... }
    ref { atomNumbers ... }

harmonic {
  colvars d
  centers X
  forceConstant X

---- ----
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>
---- ----

On Wed, Jun 17, 2009 at 12:07 PM, Jarrod Nickel<>
> I was wondering if there are any tutorials or examples of how to use
> collective variables with NAMD 2.7b1. I have looked through the User's
> and still have no idea how to set up the colvarsConfig file.
> Basically all I want to do is restrain the center of mass of a membrane. I
> am also using SMD with zero velocity on a small molecule outside the
> membrane. My goal is to hold the small molecule a set distance away from
> membrane and measure the force on it.
> Any suggestions and help would be greatly appreciated.
> Thank you in advance,
> Jarrod

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