AMBER Archive (2004)

Subject: Re: AMBER: nrespa=2

From: David A. Case (
Date: Tue Dec 21 2004 - 09:52:53 CST

On Tue, Dec 21, 2004, Marsita M wrote:
> is it okay to use nrespa=2 for vacuo simulation using distance dependent
> dielectric constant?

As the manual implies (p. 103) nrespa will have no effect on vacuum

> starting energy for MD (Nstep=0) = 6624 kcal/mol
> final energy after minimization = -3.2678E+03 kcal/mol
> how come they are so hugely different?
> for the minimization, i used constant dielectric with dielc=1
> and for the MD, i used distance dependent dielectric, dielc=4, thats the
> only difference between the runs, is is because of different types of
> dielectric being used?

It probably is because of the different electrostatic model. You can look at
the components of the energy and see if anything besides the electrostatics
has changed.


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