Re: Extra bonds-ABF

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
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.

Giacomo

On Mon, Nov 7, 2011 at 11:53 AM, Parisa Akhski <
Parisa.Akhshi_at_chem.queensu.ca> 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 - 05:24:31 CST