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Dear All,
I noticed a peculiar behavior during Widom insertion for excess chemical potential (mu excess) computation of a salt pair. This peculiarity is in the variance in mu excess. Ideally as one a…
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I've been trying to do the following:
1.Take i number of steps with `openmmtools. AlchemicalNonequilibriumLangevinIntegrator`.
2. After i steps, set the masses of a subset of the system to zero.
3.…
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Hi, we are running some FEP validation tests using BSS from [this paper](https://pubs.acs.org/doi/10.1021/ja512751q). While some ligand pairs run fine, some can't be set up without allow_ring_breaking…
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Dear all,
I am working on a large molecule model (no specific binding) with iv bolus administration in mice. With the model simulations I cannot reach the observed maximum molecule concentrations. …
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Hey,
I am using CustomNonbondedForce to compute the interaction in my system. The speed of computation is ~30-40 % slower when using CustomNonbondedForce compared to standard way. I hope this is an…
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I've been testing the acceptance rates between neighboring pairs of states and have noticed some very low values that seem to persist regardless of the number of states. I've run YANK 0.15.2 on 5 copi…
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I was using `optking` to generate a torsion scan. Many of the structures generated didn't converge and even the ones that did converge didn't look quite right. Here is a script I used:
```python
#…
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I've been experimenting with multiple timestep (MTS) GHMC integrators that make use of different splittings of direct and reciprocal space components of `NonbondedForce`. Oddly, it turns out that the …
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For nearly the same experiment (only difference is slight change in `clearance` and existence of `switch_distance`), MC states seem to not mix in ```0.16```, while it seems to work in ```0.15``` (see …
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Temporarily disabling in #228 but I think this will be important in getting larger molecules to work.