From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Jan 30 2004 - 12:28:05 CST
> > 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
here;s an example. Say you calculate an energy value for individual chain
A of -3500kcal/mol and for B -3600 kcal/mol. For the dimer you get -7105
kcal/mol. The interaction energy would be then according to the formula
above -5 kcal/mol. Normally you do not have uncertainties of less than 5%
in MD simulations (specially if you use different values for the seed). So
the -5 kcal/mol value that you get by subtracting the two is not
significant within the error bars...
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