Add long-range dispersion correction, Beutler soft-core, and LambdaSchedule.reverse()#440
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Add long-range dispersion correction, Beutler soft-core, and LambdaSchedule.reverse()#440
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This PR adds support for the long-range LJ dispersion correction (LRC), adds a new Beutler LJ soft-core form designed for absolute binding/hydration free energy simulations, and adds a
LambdaSchedule.revese()method to reverse a schedule, allowing it to be used with theswap_end_statesoption, e.g. for ring-breaking.Rather than using OpenMM to compute the LRC, which requires costly recalculation of coefficients when changing lambda and updating force parameters, we numerically compute and cache the LRC for each lambda, then apply it as a
CustomVolumeForce. When ghost atoms are present we handle the total LRC by decomposing into a "background" term and a "ghost-lrc" that adds contributions for ghost/ghost and ghost/non-ghost interactions. For GCMC simulations we handle the LRC for solvent atoms separately so that we can dynamically update the correction as water molecules are inserted or deleted from the system. Unit tests show that end-state energies for a perturbable system agree with those that would be computed by OpenMM when using LRC with theNonbondedForce. We also validate the the water LRC code works correctly by numerically comparing the change in energy for a GCMC insertion.The PR also adds a new Beutler soft-core form designed for ABFE simulations. The form matches that used by GROMACS, providing a useful reference for benchmarks simulations. In updating the soft-core I have also removed the
coulomb_poweroption, since it is incorrect for any non-zero value.Finally, the PR adds a
LambdaSchedule.reverse()method, allowing the direction of any schedule to be reversed. This is particularly useful when testing complex multi-stage schedules, e.g. ring-breaking, with theswap_end_statesdynamics option.develinto this branch before issuing this pull request (e.g. by runninggit pull origin devel): [y]