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mdin Keywords — Quick Reference

The ~50 mdin keywords most likely to come up in v1.0 workflows. Anything not listed here → see the Amber Reference Manual via manual_lookup.md.

Columns: keyword, typical values, what it does, manual section (approximate; varies by edition).

Run-control

Keyword Typical What it does Manual §
imin 0 MD; 1 minimize; 5 SP energy only Selects job type §17.5
irest 0 start, 1 restart Whether to read velocities from input rst7 §17.5
ntx 1 no velocities; 5 read velocities Input format flag (paired with irest) §17.5
nstlim depends on dt and target ps Number of MD steps §17.5
dt 0.002 (with SHAKE); 0.001 (without) MD timestep in ps §17.5
maxcyc 10000 Total min cycles (only imin=1) §17.5
ncyc 5000 Steepest-descent cycles before CG (imin=1) §17.5
numexchg depends Outer-loop count for REMD §22

Periodic-box / nonbonded

Keyword Typical What it does Manual §
ntb 0 no box; 1 constant V; 2 constant P PBC mode §17.5
ntp 0 NVT; 1 isotropic; 2 anisotropic; 3 semi-isotropic Pressure scaling §17.5
barostat 1 Berendsen; 2 Monte Carlo Barostat algorithm (only when ntp>0) §17.5
taup 2.0 ps Pressure relaxation time §17.5
cut 10.0 Å explicit; 999.0 implicit Nonbonded cutoff §17.5
iwrap 0 or 1 Wrap coordinates into the primary box §17.5

Thermostat

Keyword Typical What it does Manual §
ntt 0 constant E; 1 Berendsen; 3 Langevin Thermostat algorithm §17.5
gamma_ln 2.0 1/ps Langevin friction coefficient §17.5
tempi 0.0 for heat Initial temperature §17.5
temp0 300.0 K Target temperature §17.5
ig -1 (random) Random seed §17.5

SHAKE

Keyword Typical What it does Manual §
ntc 1 no SHAKE; 2 H bonds; 3 all bonds SHAKE bond constraints §17.5
ntf 1 all forces; 2 skip H; 3 skip all bonds Force evaluation matched to ntc §17.5

Output frequency

Keyword Typical What it does Manual §
ntpr 100 or 500 mdout print frequency (steps) §17.5
ntwx 500 (= 1 ps at dt=0.002) Trajectory write frequency §17.5
ntwr 1000 or 10000 Restart-write frequency §17.5
ntwprt 0 for full system Write only first N atoms (analysis trick) §17.5
ioutfm 1 NetCDF; 0 ASCII Trajectory format §17.5

Implicit solvent (GB)

Keyword Typical What it does Manual §
igb 0 explicit; 1, 2, 5, 7, 8 GB models Selects implicit-solvent flavor §6
gbsa 0 off; 1 LCPO surface; 2 ICOSA Solvent-accessible-surface term §6
surften 0.005 kcal/mol/Ų SASA proportionality §6
saltcon 0.150 M Salt concentration in GB §6
rgbmax 25.0 Max radius for Born-radius computation §6

Restraints

Keyword Typical What it does Manual §
ntr 1 to enable Positional restraints flag §17.6
restraintmask ':1-200&!@H=' Amber mask of restrained atoms §17.6
restraint_wt 10.0 kcal/mol/Ų Force constant §17.6
ref (-ref CLI flag) Reference rst7 for restraint coordinates §17.6
nmropt 0 off; 1 enables &wt and DISANG NMR-style time-varying restraints §28

REMD / enhanced sampling

Keyword Typical What it does Manual §
rem 0 off; 1 T-REMD Enables replica exchange (CLI flag, not mdin) §22
numexchg depends Number of exchange attempts §22
iamd 0; 1/2/3 for aMD Accelerated MD mode §27
ethreshd, alphad, ethreshp, alphap depends aMD bias parameters §27
jar 0; 1 for SMD Steered MD flag §28

Constant-pH / redox (deferred features)

Keyword Typical What it does Manual §
icnstph 0; 1/2 for cpH-MD Constant-pH MD flag §29
ntcnstph depends Frequency of protonation-state attempts §29
solvph 7.0 Simulated pH §29
icnste 0; 1 for cE-MD Constant-redox MD flag §29

QM/MM (deferred)

Keyword Typical What it does Manual §
ifqnt 0; 1 to enable QM/MM mode flag §10
qmmask mask QM region §10
qm_theory PM6, DFTB, EXTERN QM method §10
qmcharge int QM region charge §10

Anything not listed

→ See manual_lookup.md for the Amber Reference Manual link. The keyword index in the manual's appendix is the authoritative source.

Common mistakes

  • ntb=2, ntp=0 — incompatible (constant-P box without pressure scaling). Should be ntb=2, ntp=1 for NPT.
  • ntc=2, ntf=1 — partial SHAKE. Should match (both 2, or both 1).
  • igb=2, ntb=1 — implicit and explicit can't both be on. Use igb=2, ntb=0, cut=999.
  • temp0=300 with tempi unset on a heat stage — the system never ramps. Use tempi=0, temp0=300 plus a &wt TEMP0 block for the ramp.

Cross-reference

For runnable mdin templates with these keywords assembled, see scripts/_amber.py:render_min/heat/density/prod — those are the v1.0 templates and they cover the most common cases.