**From:** Jason Swails (*jason.swails_at_gmail.com*)

**Date:** Wed Apr 16 2014 - 08:27:34 CDT

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On Mon, Apr 14, 2014 at 5:25 PM, Jonathan Phillips <994phij_at_gmail.com>wrote:

*> Hi,
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*> I'm a bit confused by the manual (looking at 2.9). Was wondering if
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*> anybody could help clear up my confusion.
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*>
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*> The manual says:
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*> "NAMD uses a non-bonded pair list which contained all pairs of atoms for
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*> which non-bonded interactions should be calculated."
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*> This implies that if you have pairlistdist set to anything less than the
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*> box size, true 'full electrostatics' will never be calculated.
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*>
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No. And I think what you meant was if the cutoff was half the box size

(the cutoff will be the _radius_ of the sphere for which direct

interactions are computed).

*> You'll calculate PME (if it's on) for every pair of atoms in the
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*> pairlist (and their images in other boxes), but nothing for the atoms which
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*> aren't in the pairlist.
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*>
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No. See below for my comments about PME. What you'll be missing is the

force contributions from the van der Waals interactions outside the cutoff

(assuming NAMD uses a long-range dispersion correction, the energy and

virial will be more or less correct for "infinite" cutoffs subject to the

typical assumptions that particle density is the bulk density).

*>
*

*> But the default for pairlistdist is cutoff, and the manual says this about
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*> cutoff:
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*> "Next, consider the case where full electrostatics are calculated. In this
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*> case, the electrostatic interactions are not truncated at any distance. In
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*> this scheme, the cutoff parameter has a slightly different meaning for the
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*> electrostatic interactions — it represents the local interaction distance,
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*> or distance within which electrostatic pairs will be directly calculated
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*> every timestep."
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*> This suggests that you can get full electrostatics without setting a
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*> particularly large pairlistdist (or else they'd have mentioned pairlistdist
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*> in that section). Which then suggests that pairlistdist applies only to
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*> short range interactions.
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*>
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Correct.

*> Finally, the manual says:
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*> "PME stands for Particle Mesh Ewald and is an efficient full
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*> electrostatics method for use with periodic boundary conditions."
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*> This suggests that when PME is on, full electrostatics is used, and when
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*> PME is off, it is not used, but that's not explicitly stated.
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*>
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Ewald sums are a way of computing long-range electrostatics. For an

infinitely periodic system, you cannot possibly do a brute-force

sum-over-pairs of all atoms in all periodic cells (there are an infinite

number of atoms). So you MUST make a choice for how you include long-range

electrostatics. Ewald sums work for periodic systems with neutral unit

cells and give you the exact long-range electrostatics for the infinitely

periodic system. (PME is a special case of Ewald that uses an

interpolating charge grid so the discrete FFT can be used instead of a

traditional Fourier transform.) Ewald sums work by splitting the

electrostatic contributions up into a short-range sum in direct space (a

sum over pairs of atoms in the pairlist) and a long-range sum in Fourier

space. Together, they recover the exact, full electrostatics of the

infinitely periodic system.

So are the pair lists referring specifically to short range interactions,

*> and is my guess right about PME?
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*>
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There are other ways of "accounting" for long-range electrostatic effects

(like reaction field and isotropic periodic sum), but using a cutoff (even

with switching or shifting functions) is not one of them.

Hope this helped,

Jason

-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher

**Next message:**manish kesherwani: "Re:"**Previous message:**Norman Geist: "AW: Re: Persistent margin errors"**In reply to:**Jonathan Phillips: "full electrostatics and pairlistdist"**Next in thread:**Jonathan Phillips: "Re: full electrostatics and pairlistdist"**Reply:**Jonathan Phillips: "Re: full electrostatics and pairlistdist"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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