Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules
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Bibliographic record
Abstract
Calculations demonstrate that with a minor modification conventional ab initio effective potentials can be employed in place of link atoms to truncate quantum regions in hybrid quantum mechanics/molecular mechanics calculations. Simple quantum capping potentials are formed by replacing excess valence electrons in conventional effective potentials by spherical shielding and Pauli terms chosen to duplicate all-electron molecular structures and charge distributions. Tests involving truncated histidine show errors in charge and protonation energy to be reduced as compared to the link atom approach. Because of the use of conventional effective potential expansions, this approach can be implemented with minimal or no program modifications. Indeed, in its simplest form it requires the addition of only a single Gaussian and adjustable parameter to a conventional effective potential expansion. The parametrization requires little effective potential expertise or effort.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it