Re: [AMBER] umbrella sampling

From: Jason Swails <>
Date: Mon, 15 Oct 2012 08:07:24 -0400

On Mon, Oct 15, 2012 at 3:32 AM, Elisa Frezza <>wrote:

> Dear All,
> I would like to do umbrella sampling and to use as restraint angle the
> angle between two duplex of DNA.
> How can I do this? Can I define 4 center of mass and make the restraint
> using them?

4 coordinates are for dihedral restraints. Angle restraints use 3. If you
want to use COM restraints for angles or dihedrals, you can do this with
sander (only).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Mon Oct 15 2012 - 05:30:04 PDT
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