references

amber-chemist References — Index

Reference files are topic-scoped: read the one matching your task, not the whole index. The MD core, REMD, and add-ons are the load-bearing distinctions; everything else is supporting material or honest deferrals.

When to read which file

Core (read these first when running MD)

• md_core.md — The single-replica MD pipeline: stage rendering, restart vs extend, restraints, barostat options, implicit-solvent (GB) MD. Read when running amber_md.py or chaining stages by hand.
• remd.md — T-REMD: temperature ladder choice (geometric vs vdSpoel vs explicit), exchange-rate target (15-50%), engine selection (pmemd.cuda.MPI -rem 1), demux. Read when running amber_remd.py or before tuning a ladder.
• force_fields.md — Force-field choices: GAFF2 + AM1-BCC (v1.0 only), water models, what's deferred (ff19SB, OL21, LIPID17). Read when the prompt names a biopolymer force field.

Add-ons (read when consuming MD output)

• add_ons.md — The framing: add-ons consume the MD output, not co-equal verbs. The extension surface convention.
• analysis.md — cpptraj idioms used by amber_analyze.py (RMSD, RMSF, RDF, hbond, radgyr, ensemble for REMD demux).
• single_point.md — imin=5, maxcyc=0 snapshot SP vs cpptraj esander per-frame energies.
• scoring.md — MMPBSA / MMGBSA: input file structure, GB vs PB, alanine scan, per-residue. What MMPBSA is not.

Reference / lookup

• manual_lookup.md — Curated URLs to the Amber Reference Manual, AmberHub, tutorials, cpptraj/MMPBSA PDFs. The fast path to authoritative answers.
• mdin_keywords.md — Flat table of the ~50 most-asked mdin keywords with manual section pointers.
• cpptraj_idioms.md — Drop-in cpptraj recipes for the most common analyses.
• mmpbsa_idioms.md — Drop-in MMPBSA decks (GB, PB, alanine, per-residue, MPI).

Failure modes / deferrals / context

• failure_modes.md — Known failure modes across prep / MD / REMD / analysis / scoring, with recovery recipes.
• extension_map.md — Big Amber features not yet shipped (TI/FEP, aMD, SMD, umbrella, H-REMD, QM/MM, constant-pH, membrane, PLUMED, multi-GPU): which script each one would land in. Cite this for honest deferrals.
• carveout_relationship.md — How amber-chemist relates to ase-chemist's v1.3 carve-out. Cite when the user is on a shared-zone prompt and wonders which skill should answer.