For the protein force fields we don't fit the absolute energies, so the
offset doesn't matter.
Carlos
On Oct 19, 2015 7:30 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
> On Mon, Oct 19, 2015 at 6:25 PM, Ross Walker <rosscwalker.gmail.com>
> wrote:
>
> > Hi All,
> >
> > I am wondering if anyone knows the origin or why the dihedral term we use
> > in the AMBER force field has the 1+ term in it.
> >
> > I.e. we have:
> >
> > ndih n[i]
> > sum sum( 1/2 x Vn(1+cos(n.theta - phi)) )
> > i=1 j=1
> >
> > Specifically we have the 1+cos term in there which is I guess to make the
> > cos term oscillate between 0 and 2 rather than -1 and +1 and then we have
> > the 1/2 in front of the Vn to get rid of the 2 making it between 0 and
> Vn.
> > However, as far as I can tell this is purely cosmetic. Is that correct?
> >
>
> I always thought of it more as making it *look* a little more like the
> other bonded terms (which are harmonic, and have the 1/2 term in front of
> the force constant, and as a result have a minimum energy at 0). But
> obviously the 1+ has no effect on forces, and the 1/2 can be pulled into
> the Vn term (which, in Amber, it already is).
>
> As in I could ditch the 1/2, and ditch the 1+ and just have
> > V[i,j].cos(n.theta-phi). The question is if that is true why don't we do
> > this - does anyone know?
> >
>
> At this stage, it would be historical.
>
>
> The issue arrises not in MD but when we try and refit the torsion terms. If
> > we try to fit energies against quantum energies we always have an offset
> in
> > the mean due to the origins not matching - that doesn't matter since it
> > would be constant during an MD run. However, if we are fitting Vn terms
> the
> > 1+cos term here causes our mean to drift as we adjust Vn. This is a pain
> in
> > the butt when it comes to getting a good fit. Thus I propose to just fit:
> > Vn.cos(n.theta-phi) which, I believe would give perfectly transferable
> > parameters to the 1+cos equation.
> >
>
> Lachele actually addressed this precise problem in her presentation at the
> Amber developer's meeting last year. The solution is simple: fit the
> zero-periodicity term. That *gives* you an arbitrary constant to improve
> your fit -- it doesn't contribute to an overfitting problem and solves the
> issue you're describing. Then you're free to simply throw that term away
> when making the frcmod file since it has no effect on forces. It seems to
> me you are rediscovering her problems :). I'm sure she'd be happy to share
> her slides if she can find them and you wanted them. </throwing Lachele
> under the bus>
>
> Am I missing anything here? - Is there any reason why we couldn't go the
> > whole step and just ditch the 1/2 and 1+ terms from the entire force
> field?
> > - Seems to me all that would happen is for a given set of parameters (say
> > FF14SB) we just shift the energy origin but everything else would still
> > work.
> >
>
> A couple things. If you do a QM scan, you're certainly not going to get
> an energy of zero at the midpoint -- the zero point energy will be
> arbitrary. The easiest thing to do with your QM scan is simply scale the
> whole potential by the minimum energy value, which will give you the same
> minimum as the 1+cos() series at 0 (maybe that's why it's done?).
>
> Y
> ou can fit however you'd like, but changing how Amber computes this
> internally would break from how every other package calculates proper
> torsions. It would make cross-program conversion validation much harder
> than it currently is. This is a big deal IMO.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Oct 20 2015 - 03:30:04 PDT
