Re: Pair interaction energy

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jan 30 2004 - 12:08:38 CST

On Fri, 30 Jan 2004, Ioana Cozmuta wrote:

>
>
> On Fri, 30 Jan 2004, Sundaramoorthy, Munirathinam wrote:
>
> > Dear NAMD users,
> >
> > Alternatively, is it good enough if I calculate energies of individual
> > chains (A & B) and the dimer (AB) and use the difference [(A+B)-AB] as
> > the interaction energy?
> >
> Just a comment: you would have to subtract big numbers so you'll have
> large uncertainty on your result.
>
> Ioana
However, you could decrease your error somewhat by using a few MD runs to
shake the interface around and then make a calculation. If you follow the
logic in the first email, you would of course have to run MD on the
dimers. Although I would not expect large changes in the potential
energy.....

>

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**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
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