Thanks for that clarification - I'll have to look into modifying the lambda
scaling in nmropt instead then.
On Tue, Nov 2, 2021, 4:52 PM Jason Swails <jason.swails.gmail.com> wrote:
> In general terms this is impossible, and that's because the PME code
> computes the exceptions from the lists of bonds, angles, and torsions. If
> you used the GB code (either using a GB model or setting igb=6 to get
> vacuum electrostatics without periodic boundary conditions), then you can
> hack the exclusion list in the topology file to achieve what you want.
>
> I think you can do what you want if you're willing to use OpenMM (because
> you can control the exceptions very fine-grained), but not within sander or
> pmemd.
>
> HTH,
> Jason
>
> On Mon, Nov 1, 2021 at 2:32 PM Brian Radak <brian.radak.gmail.com> wrote:
>
> > My understanding is that adding new bonds with ParmEd is akin to adding
> new
> > force field terms such that nonbonded exclusions are updated in the
> > topology. The only difference is that a bond does not necessitate angles
> > and dihedrals as in tleap (or a defined bond type). This seems to be
> > verified by "just doing it" and checking that the energy difference is
> not
> > in the BOND term only.
> >
> > My question is - is there a way _not _ to update the exclusions so that
> the
> > new term is exactly like a harmonic restraint? This would trick the
> > bookkeeping in alchemical calculations, which apply a lambda factor to
> > nmropt terms.
> >
> > Cheers,
> > Brian
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> >
>
>
> --
> Jason M. Swails
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Received on Tue Nov 02 2021 - 20:00:02 PDT
