Re: [AMBER] V5 dihedrals

From: Jason Swails <>
Date: Wed, 16 Feb 2011 13:10:46 -0500


To add onto what Professor Case already said: sander/pmemd explicitly use
the exact cosine expressions for dihedral terms that is found in the manual
and every article describing the Amber force field. NAB and NMODE, on the
other hand, takes a different approach.

If the phase angle is 0 or 180 (0 or pi), then you can analytically expand
the cosine of any periodicity in terms of the cosine of the angle itself
using the multiple-angle formulae. For example, cos(2x) = 2 * cos^2(x) -
1. These formulae are trivially derivable using Euler's equation (e^(i * x)
= cos(x) + i sin(x)) and can allow for faster and more stable evaluation of
these dihedral terms (in addition to making derivatives much easier to
take). Whether the value is 0 or pi simply determines what sign the term is
supposed to have (as can be verified with Euler's equation, again). The
dihedral formulae cannot be so simply reduced for phase angles not equal to
0 or pi, so NAB/NMODE defaults back to the way sander does it for these
cases (which are atypical). Up until the release of ff99SBildn, a
periodicity of 5 was never encountered in Amber force fields, so the nab
architects never bothered deriving/implementing that case -- they stuck with
periodicities of 1, 2, 3, 4, and 6. As Professor Case mentioned, the
periodicity 5 case was recently derived and implemented (and fixed up) in
the development version, and should be released as a patch after we've been
able to run it through some tests.

What this means is that sander and pmemd can handle an arbitrary periodicity
regardless of what phase angle is assigned. However, if a phase angle is
assigned a value of 0 or pi, then NAB and NMODE can only accept values of 1,
2, 3, 4, (in the future 5,) and 6 as allowable periodicity values. The
tolerance, meaning how much the periodicity is allowed to differ from 0 or
pi in terms of radians, is 0.01 (which is ~0.6 degrees).

The reason for all of this possibly useless information is to demonstrate a
temporary workaround for this limitation in NAB and NMODE -- adjust the
phase slightly (by at least 0.6 degrees) for terms where the periodicity is
equal to 5 until a fix comes out. I can't guarantee it'll work, but based
on the limited code investigation I did I think it will.

Good luck!

On Wed, Feb 16, 2011 at 12:14 PM, case <> wrote:

> On Wed, Feb 16, 2011, wrote:
> >
> > I would like to know if Sander in Amber10 or Amber11 can handle dihedral
> > potentials described with additional coefficients in a frcmod file (i.e.,
> V5
> > besides V1, V2, V3 and V4).
> As far as I can see, there is no problem with sander (or with pmemd). The
> nmode and nab codes need an update, which we are working on.
> ...dac
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Wed Feb 16 2011 - 10:30:04 PST
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