Re: collective variables

From: Cesar Millan (pachequin_at_gmail.com)
Date: Wed Jun 17 2009 - 15:29:02 CDT

Hi Giacomo, i have two related questions : a) what happend if you want to
use a rms parameter instead of distance? b) I suppose that the X value that
you assign must be related to the metadynamics protocol, how do you assign
this value?

Thank you for your help.

Cesar

On Wed, Jun 17, 2009 at 1:26 PM, Giacomo Fiorin <gfiorin_at_seas.upenn.edu>wrote:

> 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--000e0cd20ddc5555fe046c9124ab--

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