Amber中的一些option设置及名词

详细请见AMBER官方文档第18章第6节（18.6）

Amber16.pdf

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