Re: [AMBER] van der Waals interactions, electrostatic interactions and long-range corrections

From: David A Case <>
Date: Tue, 6 Mar 2018 18:47:57 -0500

On Tue, Mar 06, 2018, balaahme wrote:
> 1. I have chosen for the cutoff distance for nonbonded interactions
> to be 8 angstroms. Does this apply to both van der Waals and
> electrostatic interactions?

It's a bit more complex than that:

   a. for electrostatic interactions, "cut" determines how the
electrostatic forces (in a periodic simulation) are distributed between
"direct" and "reciprocal" terms. The sum of these two is remarkably
(but not completely) independent of the value of cut.

  b. for Lennard-Jones interactions, "cut" is indeed a cutoff; there is
a continuum term for interactions beyond the cutoff (controlled by
the "vdwmeth" paramter,) and turned on by default. This is fairly
accurate for isotropic systems, much less so for for strongly anisotropic

> 2. I do not think I have included any keywords that invoke a change
> to the long-range correction calculation. By default, is there any
> long-range correction that is applied?

It would be appropriate to call the long-range LJ term a "correction" to
the cutoff result. It's not correct to think of the reciprocal space
contribution as a "correction" for electrostatics: the direct and
reciprocal parts are tied intimately together.

> Therefore, I want to check that, by default, the PME summation method is
> performing long-range corrections to electrostatic interactions.

PME is on by default for periodic simulations. See above for
considerations about the word "correction".

...hope this helps...dac

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Received on Tue Mar 06 2018 - 16:00:03 PST
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