AMBER Archive (2008)

Subject: Re: AMBER: twin cut-off radii

From: Robert Duke (rduke_at_email.unc.edu)
Date: Mon Feb 04 2008 - 10:55:06 CST

I did not see the beginning of this thread, or somehow deleted it. There
are twin cuts in pmemd in explicit solvent, but the twin cuts there are in a
pme context. So one of the cuts applies to electrostatics, with everything
inside the cut being handled by a direct force computation, and everything
outside the cut being handled by a reciprocal space pme calc; as Dave says,
ALL electrostatic interactions are accounted for. What pme then introduces
in terms of twin cuts is the ability to extend the range of vdw interactions
further than the direct electrostatic cutoff. Traditionally, vdw
interactions have just been cut off at the pme direct space electrostatics
cutoff, and the vdw interaction falls off sufficiently rapidly that this is
generally not a big deal. Still, folks do find that they want to measure
vdw interactions out to say 9 angstrom or even further, whereas more
efficient pme calcs can be done with a direct electrostatics cutoff of say
between 8 and 7 angstrom. So pmemd implements this capability (with the
vdw_cutoff always >= es_cutoff). I had considered not continuiing to
support this at some points during development because it is a pain to
maintain, but have received feedback that some folks really find it useful.
It works best with tip3p and similar water models that don't have vdw
interactions on the H atoms.
Regards - Bob Duke

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
To: <amber_at_scripps.edu>
Sent: Monday, February 04, 2008 11:09 AM
Subject: Re: AMBER: twin cut-off radii

> On Mon, Feb 04, 2008, Sandeep Kaushik wrote:
>
>> I want to simulate a protein to which i have added two metal ions. The
>> system has been solvated using explicit water. The problem that i am
>> facing
>> is the in order to include the effect of the ion on residues which are
>> about 20 A apart i need the cut-off radius to be around 20 A.
>
> This statement is not the case. *All* electrostatic interactions are
> computed
> in explicit water simulations. The value of "cut" only serves to make a
> division between those interactions computed via direct sum, and those
> computed via the "reciprocal" sum. So you are just shooting yourself in
> the
> foot to try to run with a 20 Ang. cutoff.
>
> ....dac
>
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