Re: [AMBER] NAB: pbc calculations available after all?

From: Josh Berryman <>
Date: Mon, 26 Jul 2010 16:24:57 +0200

Thanks for the preview. I'll just ignore long-range forces for now and make
sure to set things up so that new electrostatics methods can be swapped in
easily once everything else works.


On Mon, Jul 26, 2010 at 4:03 PM, case <> wrote:

> On Mon, Jul 26, 2010, Josh Berryman wrote:
> > Hello everyone... I am trying to build a NAB application, and am prepared
> to
> > extend it a little bit to add PBCs if needs be; but I notice that with
> the
> > settings:
> >
> > #define MM_OPTIONS ("gb=0, cut=12.0, tautp=24, temp0=300.0,
> ntpr=1,
> > ntpr_md=1, ntwx=10")
> >
> > That periodic imaging does actually seem to work already, albeit for the
> > solvent only (which is fine if the solute stays centred). *nbond_box*
> and *
> > nblist_box* are the functions called,
> > and to a cursory check everything seems fine.
> >
> > The documentation says that:
> >
> > "periodic simulations are not (yet) supported" ... does that mean that
> they
> > are there, but undocumented, or that there is some serious pitfall
> waiting
> > for me if I run this kind of calculation?
> There are serious pitfalls. Note that the long-range part of
> electrostatics usually provided by PME is not included in the code you
> saw, which started as a primitive attempt to support periodic simulations
> using ips. If you were *very* careful, you might get an IPS calculation
> working: check the amber11/AmberTools/test/nab/Run.ips script for a simple
> test case. But there are all kinds of rough edges: I'm not sure the
> forces are correct, not sure that it works correctly in parallel, quite
> sure that the nonbond list is horribly inefficient, won't work with extra
> points, has no support for constant pressure simulations, etc., etc.
> [Incidentally, I don't see any restriction in the code to solvent only--in
> fact, it should not know the difference between "solute" and "solvent". If
> there is such a limitation, it's a bug.]
> We are working toward releasing the mdgx program described here:
> %T Multi-Level Ewald: A Hybrid Multigrid/Fast Fourier Transform Approach to
> the Electrostatic Particle-Mesh Problem
> %A D.S. Cerutti
> %A D.A. Case
> %P 443-458
> %J J. Chem. Theory Comput.
> %V 6
> %D 2010
> Right now, this is not very well integrated into NAB/sff (it's written as a
> stand-alone code). It's much better tested, but getting it documented has
> been slow, as is incorporating key features like extra points. It's easy
> to
> see why it took many years to get sander and pmemd to the place where they
> are
> now...going from "proof of principle" to a code that can be used for
> serious
> simulations is big jump.
> ....dac
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Received on Mon Jul 26 2010 - 07:30:06 PDT
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