*
I would very much appreciate receiving AMBER users' opinions on the
best way to set the dielectric multiplicative constant (DIELC) when
running simulations explicitly in water and using eedmeth=5 (IDIEL=1
for earlier versions and sander_classic) and periodic
boundary conditions. Assuming that the dielectric constant of water
is 80, how does one set up the simulation for this?
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I find the dielectric in molecular simulations a rather interesting object as well. The general concensus is that if you've including water explicitly then you should be using a dielectric of 1 since the explicit water will produce the required dielectric of 80 on its own accord. If you are not including explicit water then using a straight dielectric of 80 ( ie, not distance dependent ) seems to be invalid for three reasons.

- It's a time averaged quantity. That is the dielectric of water is frequency dependent and hence should be different for different frequency motions.
- It's a space averaged quantity, ie macroscopic. So it shouldn't be applied between things only nm apart, which is obvious in the limiting case of two atoms only a few angstrongs apart and hence with a vacuum between them.
- Bound surface water around a protein does not have the same dielectric as bulk water, so shouldn't be modelled as such.

On the distance dielectric model, for a particular protein BPTI, Guenot and Kollman showed in this paper,

*J. Comp. Chem*, **14**(3),295--311 (1993)

that the distance dielectric model with a finite cutoff provided a closer average conformation to the explicit water model with an infinite cut-off than did any of the explicit water models with finite cut-offs. So the distance dielectric model gets a vote of confidence.