详细请见AMBER官方文档第18章第6节（18.6）
The settings can be summarized as follows:
imin=1 Choose a minimization run
ntx=1 Read coordinates but not velocities from ASCII formatted Inpcrd coordinate file
irest=0 Do not restart simulation
maxcyc=2000 Maximum minimization cycles
ncyc=1000 The steepest descent algorithm for the first 0-ncyc cycles, the switches the conjugate gradient algorithm for ncyc-maxcyc cycles
ntpr=100 Print to the Amber mdout output file every ntpr cycles
ntwx=0 No Amber mdcrd trajectory file written (not applicable to minimization)
cut=8 Nonbonded cutoff distance in Angstroms (for PME, limit of the direct space sum - do NOT reduce this below 8.0. Higher numbers give slightly better accuracy but at vastly increased computational cost.)
imin=0 Choose a molecular dynamics (MD) run [no minimization], turn off minimization
nstlim=10000 Number of MD steps in run (nstlim * dt = run length in ps)
dt=0.002 Time step in picoseconds (ps). The time length of each MD step
ntf=2 Setting to not calculate force for SHAKE constrained bonds
ntc=2 Enable SHAKE to constrain all bonds involving hydrogen
tempi=0 Initial thermostat temperature in K (see NMROPT section)
temp0=300.0 Final thermostat temperature in K (see NMROPT section)
ntwx=1000 Write Amber trajectory file mdcrd every ntwx steps
ntb=1 Periodic boundaries for constant volume
ntp=0 No pressure control
ntt=3 Temperature control with Langevin thermostat
ntr=1 ntr>0 restrain specified atoms: restraintmask & restraint_wt Default = 0
gamma_ln=2.0 Langevin thermostat collision frequency
nmropt=1 NMR restraints and weight changes read (see NMROPT section)
ig=-1 Randomize the seed for the pseudo-random number generator [always a good idea unless you are debugging a simulation problem]
ntx=5 Read coordinates and velocities from unformatted inpcrdcoordinate file
irest=0 Flag to restart a simulation. 0, (default) Do not restart the simulation, run as a new simulation 1, restart the simulation, reading coordinates and velocities from a previously saved restart file. if irest=1, ntx must be 4 or higher
temp0=300.0 Thermostat temperature. Run at 300K
ntb=2 Use periodic boundary conditions with constant pressure
ntp=1 Use the Berendsen barostat for constant pressure simulation
taup=1.0 Pressure relaxation time (in ps). The recommended value is between 1.0 (default) and 5.0 psec
ntb=0 disable periodicity
igb=0 not using implicit or explicit solvent
Some of the important values include in .out file:
NSTEP The time step that the MD simulation is at
TIME The total time of the simulation (including restarts)
TEMP System temperature
PRESS System pressure
Etot Total energy of the system
EKtot Total kinetic energy of the system
EPtot Total potential energy of the system