Ref: http://ambermd.org/doc12/Amber18.pdf, Page 320 ====== Basic and Input/Output ====== ^ Calculation Type ^^^ ^ name ^ default ^ description ^ | imin | 0 | 0: No minization \\ 1: Energy minimization \\ 5: Read in a trajectory for analysis | | nmropt | 0 | 0: No NMR optimization\\ 1: NMR restraints, weight changes \\ 2: NMR restraints, weight changes, NOE vol, CS, RDC | ^ Input ^^^ ^ name ^ default ^ description ^ | ntx | 1 | 1: Only read coordinates \\ 5: Coordinates; Box information(//ntb//>0); velocities(//irest//=1) | | irest | 0 | 0: New simulation \\ 1: Restart the simulation, read saved restart file(//ntx//>=4) | ^ Output ^^^ ^ name ^ default ^ description ^ | ntxo | 2 | 1: Output as text file \\ 2: Output as bindary NetCDF file | | ntpr | 50 | Step to print energy information as "mdout" and "mdinfo" file | | ntwx | 0 | Step to write coordinates to the "mdcrd" file, no coordinate trajectory(//ntwx//=0) | | ntwprt | 0 | 0: Include all atoms when writing trajectories \\ >0: Include only atoms 1 to //ntwprt// | | idecomp | 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 ====== ^ Frozen or Restrained atoms ^^^ ^ name ^ default ^ description ^ | ntr | 0 | >0: Atoms strained by a harmonic potential in Cartesian space | | restraint_wt | | The weight (in kcal/mol −Å²) for the positional restraints | | restraintmask | | String that specifies the //restrained// atoms when //ntr//=1 | ^ Energy minimization ^^^ ^ name ^ default ^ description ^ | maxcyc | 1 | The maximum number of cycles of minimization | | ntmin | 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 | | dx0 | 0.01 | The initial step length | ====== Dynamics Simulation ====== ^ Molecular dynamics ^^^ ^ name ^ default ^ description ^ | nstlim | 1 | Number of MD-steps to be performed | | ntmin | 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 | | dx0 | 0.01 | The initial step length | | dt | 0.001 | Recommended MAXIMUM is .002 if SHAKE is used, or .001 if it isn’t | ^ Temperature regulation ^^^ ^ name ^ default ^ description ^ | ntt | | | | temp0 | | | | tautp | | | | gamma_ln | | | | vlimit | | | ^ Pressure regulation ^^^ ^ name ^ default ^ description ^ | ntp | | | | barostat | | | | pres0 | | | | taup | | | | vlimit | | |