Re: [AMBER] Dielectric constant for dna-ligand in TIP3P system

From: Thomas Cheatham <>
Date: Tue, 17 Mar 2015 09:40:36 -0600 (MDT)

> I want to calculate the electrostatic interaction energy for a DNA-Ligand
> system in explicit TIP3P water.
> where, E=k·q1·q2/r and k (=1/4πε) and value of k = 332.24 for
> converting the energy in Kcal/mol.
> Here i want to know that dielectric constant that will be used for
> dna-ligand in explicit TIP3P water system is (~60). So, am i right that the
> final E=k·q1·q2/r*60 Kcal/mol for my system.

As Jason points out, in explicit water you would want to set the
dielectric constant to 1 since the effective dielectric screening is done
by the explicit TIP3P waters, i.e. at short range there is no screening
(since a water cannot fit between the close point charges); at longer
range, bulk water will effectively screen by ~80 (i.e. you do not have to
screen artificially by setting the dielectric constant is 80). If you did
not have explicit water (i.e. you stripped it), you could apply a distance
dependent screening (as was done in the old days) or even a more
complicated sigmoidal screening, however this gets complicated with
heteregenous systems (with differential screening), large solutes, etc.
If a heterogeneous system, likely better is to use an implicit solvent
like generalized Born (after stripping the water, as per MM-GBSA).

Based on the discussion above, the "dielectric" constant for a atomic /
molecular system is misleading since it is bulk property and is likely not
constant at atomic/molecular scales.


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Received on Tue Mar 17 2015 - 09:00:03 PDT
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