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NH₃–CH₃Cl PhysNet results

Placeholder — run the example pipeline to populate metrics and figures:

source examples/m/_env.sh
bash examples/m/run_all.sh

See examples/m/README.md. Checkpoint and dataset: commit 30eb7a01f7fcf1d42a795f188526a80e547110fd (examples/m/kl.json, examples/m/nh3_ch3cl_filtered.npz).

NEB (vacuum ML path)

ASE nudged elastic band on kl.json between reactant / product XYZs under examples/m/neb/. Guide: Nudged elastic band.

source examples/m/_env.sh
bash examples/m/13_neb.sh
# or: uv run mmml neb --config examples/m/yaml/neb.yaml --overwrite

ADUMB (PyCHARMM)

Example RCs Config Script
1D bond difference rdif = (r_{\mathrm{ClC}}-r_{\mathrm{CN}}) ∈ [-6, 6] Å (SN2 ~[-3, 3]) examples/m/yaml/adumb_nc_distance.yaml 09_adumb_nc_distance.sh
2D Cl⋯C / C⋯N rcl, rcn distances yaml/adumb_clc_cn_2d.yaml 10_adumb_clc_cn_2d.sh
1D + TIP3 same rdif (PBC skeleton) yaml/adumb_nc_distance_tip3.yaml SOLVATED=1 on 09_*.sh

Optional USE_NPZ_PDB=1 feeds 07_export_solute_pdb.py geometry. The 1D RC is an RXNCOR combination of two distances (CHARMM COMBI_TYPE): (\xi = r_{\mathrm{ClC}} - r_{\mathrm{CN}}). For 2D, define two distances, rxncor set nrxn 2 …, two umbrella rxncor … name … cards, then one umbrella init. ADUMB NAME tokens are ≤4 characters (rdif, rcl, rcn).

CHARMM build

  • Pref keys: ADUMB + ADUMBRXNCOR (?ADUMBRXN == 1). scripts/rebuild_charmm_mlpot.sh enables ADUMBRXNCOR by default.
  • Without ADUMBRXNCOR, umbrella rxncor prints Unknown umbrella specified and heat often SIGSEGVs under MLpot/MPI.
  • Prefer umbrella rxncor … min 0.0 max … when libcharmm is unpatched. Unpatched UM1RXN treated the upper edge as (max − min) for any nonzero min (e.g. min 2 max 6 → abort once value (> 4); min -3 max 3 → upper check against 6 instead of 3). mmml patches that check to [min, max]. The 1D difference example uses min -6 max 6 (matches component RESD walls; SN2 band ~[-3, 3]).
  • Reactivity: RESD walls are soft outer caps (~7.25 Å) and do not forbid SN2. The CGenFF BOND C1–CL1 (k≈220 in par_ch3cl.prm) does — CHARMM bonded terms remain in ENER INTERN even with include_mm: false. The 1D YAML delete bond/angle removes C–Cl before heat. Do not replace the system with a product topology that has a hard C–N bond (same trap, other basin). Optional: MMML_ADUMB_RC_WALL_BACKEND=off to A/B-test walls.

Align umbrella init with heat length

Adaptive umbrella expects the dynamics length to match the WHAM schedule:

[ n_{\mathrm{step}} = \mathrm{round}(ps_\mathrm{heat} \times 1000 / dt_\mathrm{fs}) ]

[ n_{\mathrm{sim}} \times \mathrm{update} = n_{\mathrm{step}} ]

Mode dt_fs ps_heat (n_{\mathrm{step}}) Example umbrella init
Smoke 1.0 0.2 200 nsim 4 update 50 equi 25
Medium (current YAML) 1.0 100 100 000 nsim 100 update 1000 equi 200
Longer heat 1.0 1000 1 000 000 nsim 1000 update 1000 equi 500 (tune)
Longer @ 0.5 fs 0.5 1000 2 000 000 retune so nsim * update == nstep

Also keep umbrella temp near the thermostat target, and open ADUMB-WUNI.DAT / UMBCOR / RXNCOR_TRACE.DAT under the job output_dir (YAML uses basename OPEN names; lingo runs with cwd=output_dir).

Wipe {output_dir} (or at least next_run.* and pycharmm_pre_dynamics_lingo.inp) before switching smoke ↔ long heat so a leftover resume does not re-launch the wrong schedule. Stale staged lingo is a common cause of UM1RXN reaction coordinate out of range after editing umbrella rxncor min/max in the YAML — confirm the staged file has min 0.0 before trusting a long heat.

Expected artifacts (smoke)

1D — artifacts/nh3_ch3cl/adumb_nc_distance/ (ps_heat=100):

  • pycharmm_pre_dynamics_lingo.inp with combination rcl 1.0 rcn -1.0, name rdif
  • ADUMB-WUNI.DAT, UMBCOR, RXNCOR_TRACE.DAT (or lowercase)
  • heat restart / DCD

2D — artifacts/nh3_ch3cl/adumb_clc_cn_2d/:

  • lingo with nrxn 2, two umbrella rxncor cards (r_cl, r_cn)
  • ADUMB-WUNI.DAT, UMBCOR, RXNCOR_RCL.DAT, RXNCOR_RCN.DAT
  • heat restart / DCD

Results (fill in after a successful run)

Pending — paste pass criteria, RC trace summary, and figure paths here once smoke or production heat completes.

Run Config RCs (ps_\mathrm{heat}) Exit Notes / figures
1D / 2D