Re: How to restraint pairinteractions

From: Giacomo Fiorin (
Date: Fri Jun 01 2012 - 00:20:05 CDT

OK, so you want to use the interaction energy as reaction coordinate. What
interaction terms do they have: just vdW and Coulomb, or do they share any
bonds, angles, torsions, etc?

Both Tcl and colvars can do what you want, but you'll need to fetch the
charges, the vdW radii, the force constants, and sum all the potential
energy terms atom by atom, to construct your coordinate. BIG problem is:
you have explicitly solvent in between, which makes your interaction energy
of the two residues in vacuo less meaningful.

Or, you can use any reaction coordinate that gives you a good PMF (a
classic distance?), and then plot the free energy with respect to the
interaction energy? In analysis, you can plot anything versus anything, so
you'll have many more options to generate the DeltaF vs. DeltaE that you're
looking for.


On Thu, May 31, 2012 at 12:29 PM, Family Xu <> wrote:

> Hi Giacomo, Sorry for the confusion. The pairinteraction which I want to
> be the reaction coordinate of PMF is the interaction energy between two
> group atoms (for example, the interaction energy between two residues).
> Hope this is clear now.
> Thanks.
> Sanxing
> On Wed, May 30, 2012 at 5:15 PM, Giacomo Fiorin <>wrote:
>> Hello Sanxing, can you please write in more detail what do you mean by
>> "pairinteractions"? It may very well be that you can do this easily, both
>> with colvars and with tclForces.
>> On Wed, May 30, 2012 at 6:01 PM, <> wrote:
>>> Dear NAMD users,
>>> I am trying to run NAMD simulation to generate the PMF with
>>> pairinteractions as a reaction coordinate.
>>> One way to do this is to use the colvar module in NAMD, umbrella
>>> sampling followed by WHAM. Unfortunately, in terms of the user guild of
>>> NAMD, pairinteraction is not the predefined colvar in NAMD.
>>> Therefore, I am wander if this can be done by using the user defined
>>> force (tclforce). But I don't know how. Could you please let me know
>>> whether you have any suggestions to solve this issue?
>>> Thanks.
>>> Sanxing

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