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