AMBER Archive (2004)

Subject: Re: AMBER: nrespa=2

From: Carlos Simmerling (
Date: Tue Dec 21 2004 - 09:54:15 CST

> and another question, how come the starting energy of my MD simulation
> (Nstep=0) and the final energy of the minimized structure (the input
> rst file to the MD run) are different?
> 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?

you say starting "energy" for MD - is it the potential energy

SANDER writes the energy components for the minimization
and MD, you should check your output and see where the differences are.
It should be very easy to tell if it is in the electrostatics.
yes, a dielectric change from 1 to 4 can make a very large difference.

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