The procedure is the same...
Interaction energy is the difference between the energy of the full system and 
the sum of the energies of its components.
It is in general a manybody quantity.. If you ASSUME that it derives from a two 
body potential (with a given angular and radial dependence) you can estimate 
this function from a series of calculations in different configurations. This 
is just an approximation, though.

stefano 
(sent from my phone)

> On 19 Jan 2014, at 14:58, Manuel Fernandes <0occam at gmail.com> wrote:
> 
> Dear Stefano,
> 
> Many thanks for your response. The issue is that I would like to know this 
> answer when the molecules are within a crystal environment so that they are 
> interacting with many neighbours and not just interacting with each other.
> 
> Kind regards,
> 
> Manuel
> 
> Date: Fri, 17 Jan 2014 15:39:49 +0100
> From: stefano de gironcoli <degironc at sissa.it>
> Subject: Re: [Pw_forum] Interaction energies between molecules
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <52D940B5.8080704 at sissa.it>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> the way to compute the interaction energy between two fragments is to
> compute the two fragments together and compare with the energy of the
> two separated fragments.
> 
> stefano
> 
> On 01/17/2014 10:32 AM, Manuel Fernandes wrote:
> > Hi everyone,
> >
> > Is there anyway to do a lattice energy calculation on an organic
> > crystal and then extract the interaction energy between pairs of
> > molecules of interest from that? What I would like to know for example
> > is how strongly a molecule as a whole interacts with its neighbours in
> > particular directions in a crystal environment.
> >
> > Thanking you in advance,
> >
> > Manuel Fernandes
> >
> >
> >
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