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Ref: http://ambermd.org/doc12/Amber18.pdf, Page 320

====== Basic and Input/Output ======

^ <fc #f0e68c><fs large>Calculation Type</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>imin</fc> | 0 | 0: No minization \\ 1: Energy minimization \\ 5: Read in a trajectory for analysis |
| <fc #98fb98>nmropt</fc> | 0 | 0: No NMR optimization\\ 1: NMR restraints, weight changes \\ 2: NMR restraints, weight changes, NOE vol, CS, RDC |

^ <fc #f0e68c><fs large>Input</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>ntx</fc> | 1 | 1: Only read coordinates \\ 5: Coordinates; Box information(//ntb//>0); velocities(//irest//=1) |
| <fc #98fb98>irest</fc> | 0 | 0: New simulation \\ 1: Restart the simulation, read saved restart file(//ntx//>=4) |

^ <fc #f0e68c><fs large>Output</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>ntxo</fc> | 2 | 1: Output as text file \\ 2: Output as bindary NetCDF file |
| <fc #98fb98>ntpr</fc> | 50 | Step to print energy information as "mdout" and "mdinfo" file |
| <fc #98fb98>ntwx</fc> | 0 | Step to write coordinates to the "mdcrd" file, no coordinate trajectory(//ntwx//=0) |
| <fc #98fb98>ntwprt</fc> | 0 | 0: Include all atoms when writing trajectories \\ >0: Include only atoms 1 to //ntwprt// |
| <fc #98fb98>idecomp</fc> | 0 | 0: Don't decompose energies \\ 1: Decompose on a per-residue basis; 1-4 EEL + 1-4 VDW are added to internal (bond, angle, dihedral) energies \\ 2: Decompose on a per-residue basis; 1-4 EEL + 1-4 VDW are added to EEL and VDW \\ 3: Decompose on a pairwise per-residue basis; otherwise equivalent to //idecomp// = 1. Not available in TI simulations \\ 4: Decompose on a pairwise per-residue basis; otherwise equivalent to //idecomp// = 2. Not available in TI simulations|

====== Restraints and Energy minimization ======

^ <fc #f0e68c><fs large>Frozen or Restrained atoms</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>ntr</fc> | 0 | >0: Atoms strained by a harmonic potential in Cartesian space |
| <fc #98fb98>restraint_wt</fc> |  | The weight  (in kcal/mol −Å<sup>2</sup>) for the positional restraints |
| <fc #98fb98>restraintmask</fc> |  | String that specifies the //restrained// atoms when //ntr//=1 |

^ <fc #f0e68c><fs large>Energy minimization</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>maxcyc</fc> | 1 | The maximum number of cycles of minimization |
| <fc #98fb98>ntmin</fc> | 1 | 0: Full conjugate gradient minimization \\ 1:  //NCYC// cycles(default 10) of steepest descent, then switch to conjugate gradient \\ 2:  Only the steepest descent method\\ 3: XMIN method \\ 4:  LMOD method |
| <fc #98fb98>dx0</fc> | 0.01 | The initial step length |

====== Dynamics Simulation ======

^ <fc #f0e68c><fs large>Molecular dynamics</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>nstlim</fc> | 1 | Number of MD-steps to be performed |
| <fc #98fb98>ntmin</fc> | 1 | 0: Full conjugate gradient minimization \\ 1:  //NCYC// cycles(default 10) of steepest descent, then switch to conjugate gradient \\ 2:  Only the steepest descent method\\ 3: XMIN method \\ 4:  LMOD method |
| <fc #98fb98>dx0</fc> | 0.01 | The initial step length |
| <fc #98fb98>dt</fc> | 0.001 | Recommended MAXIMUM is .002 if SHAKE is used, or .001 if it isn’t |

^ <fc #f0e68c><fs large>Temperature regulation</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>ntt</fc> |  |  |
| <fc #98fb98>temp0</fc> |  |  |
| <fc #98fb98>tautp</fc> |  |  |
| <fc #98fb98>gamma_ln</fc> |  |  |
| <fc #98fb98>vlimit</fc> |  |  |

^ <fc #f0e68c><fs large>Pressure regulation</fs></fc> ^^^
^ name ^ default ^ description ^
| <fc #98fb98>ntp</fc> |  |  |
| <fc #98fb98>barostat</fc> |  |  |
| <fc #98fb98>pres0</fc> |  |  |
| <fc #98fb98>taup</fc> |  |  |
| <fc #98fb98>vlimit</fc> |  |  |
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