Re: Extra bonds-ABF

From: Giacomo Fiorin (
Date: Mon Nov 07 2011 - 11:01:22 CST

Hi Parisa, if you want to have a distance restraint between two atoms, and
you're already using the colvars module, you can create a distance variable
and apply a restraint from there. This way the force applied to the two
atoms by this restraint won't be counted in the ABF-reconstructed PMF.


On Mon, Nov 7, 2011 at 11:53 AM, Parisa Akhski <> wrote:

> **
> Dear NAMD experts,
> I need to use "extra bond" in ABF calculations to keep the distance
> between two atoms fixed. In the manual it says "the energies from extra
> bonded terms are included with the normal bond, angle and dihedral energies
> in NAMD output". I am wondering if this means the K value I use as the
> spring constant affects the results of force calculation by ABF? If so, is
> there any way to know the contribution of the "extra bond" force in ABF
> output force separately?
> Thanks,
> Parisa

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:57:54 CST