From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
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>_gmail.com
web: http://www.cmm.upenn.edu/
---- ----
On Wed, Jun 17, 2009 at 12:07 PM, Jarrod Nickel<jarrod.nickel.17_at_gmail.com>
wrote:
> 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
Guide
> 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
the
> membrane and measure the force on it.
> Any suggestions and help would be greatly appreciated.
>
> Thank you in advance,
> Jarrod
>
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