Re: [AMBER] What Can I do for Mixture of Solutions simulation and what should I assign epsilon value for this?

From: David A Case <>
Date: Tue, 18 Feb 2020 11:17:33 -0500

On Tue, Feb 18, 2020, Erdem Yeler wrote:

>I want to simulate protein-ligand interaction in 70%water -30%ethanol
>(percents for volume) For this;
>1) Should assign "epsin" in input files? For example epsin = 80 #for water

epsin is the "internal" dielectric (that is, inside the protein). It
would not be an appropriate parameter to describe the solvent.

Amber GB models have generally only been calibrated using epsin=1.

Even if you decide to use epsout (not epsin), a mixed methanol/water
solvent is only approximately characterized by its dielectric constant.
Upshot is that you should understand that you are making significant
(and mostly untested) approximations to try to treat methanol/water as a
dielectric continuum. But as long as you are looking for general
trends, trying things might be informative. You are likely to find
that an external dielectric of 62 is not much different than 78, at
least for a lot of solutes.

....good luck....dac

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Received on Tue Feb 18 2020 - 08:30:02 PST
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