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 - 14:00:02 PDT
