Equiblium system (200 - 2000 ps) &cntrl ! Nature and format of the input -------------------------------------------- ntx=5, ! Option to read the initial coordinates, velocities and ! box size form the "inpcrd" file. Option 1 must be used ! when one is starting from minimized or model-built ! coordinates. If an MD restrt file is used as inpcrd, then ! option 5 is generally used. ! =1 (default) Coordinates, but no velocities, will be read ! =5 Coordinates and velocities will be read. Box ! information will be read if ntb>0. The velocity ! information will only be used if irest=1. irest=1, ! Flag to restart a simulation ! =0 (default) Do not restart the simulation; instead, run ! as a new simulation. Velocities in the input ! coordinate file, if any, will be ignored, and the time ! step count will be set to 0 unless overridden by t. ! =1 Restart the simulation, reading coordinates and ! velocities from a previously saved restart file. The ! velocity ifnromation is necessary when restarting, so ! ntx must be 4 or higher if irest=1. ! Nature and format of the output ------------------------------------------- ntxo=2, ! Format of the final coordinates, velocities, and box size ! written to file "restrt". ! =1 (default) Formatted ASCII ! =2 Binary NetCDF file (recommended) ntpr=5000, ! Every NTPR steps energy information will be printed in ! human-readable form to files "mdout" and "mdinfo". ! Default 50. ntwr=200000, ! Every NTWR steps during dynamics, the "restrt" file will ! be written, ensuring that recovery from a crash will not ! be so painful. ! If ntwr<0, a unique copy of the file, "restrt_", ! is written every abs(ntwr) steps. Default 500. ! ntwr > 100000 is ideal for CUDA simulations !iwrap=0, ! If iwrap=1, the coordinates written to the restart and ! trajectory files will be "wrapped" into a primary box. ! This means that for each molecule, its periodic image ! closest to the middle of the "primary box" will be the ! one written to te output file. Performing such wrapping ! has no effect on the energy or forces but can mess up ! diffusion and other calculations. ! For very long runs, settings iwrap=1 may be required to ! keep the coordinate output from overflowing the ! trajectory and restart file formats, especially if ! trajectories are written in ASCII format. Default 0. ntwx=5000, ! Every NTWX steps the coordinates will be written to file ! "mdcrd". NTWX=0 inhibits all output. Default 0. ioutfm=1, ! The format of coordinates and velocity trajectory files ! (mdcrd, mdvel and inptraj). ! =0 (default) Formatted ASCII ! =1 Binary NetCDF file (recommended) !ntwprt=0, ! The number of atoms to include in trajectory files. ! This can be used to decrease the size of the files, by ! including only the first part of the system, which is ! usually of greater interest. If ntwprt=0, all atoms will ! be included. ! =0 (default) Include all atoms of the system ! =1 Include only atoms 1 to ntwprt of the system ! Molecular dynamics -------------------------------------------------------- nstlim=1800000, ! Number of MD-steps to be performed. Default 1. dt=0.002, ! The time step (psec). Recommended maximum is 0.002 if ! SHAKE is used, or 0.001 if it isn't. Note that for ! temperatures above 300K, the step size should be reduced ! since greater temperatures mean increased velocities and ! longer distance traveled between each force evaluation. ! Default 0.001. ! Temperature regulation ---------------------------------------------------- ntt=3, ! Switch for temperature scaling. [p. 289 Amber 14] ! = 0 Constant total energy classical dynamics ! = 1 Constant temperature, the weak-coupling algorithm. ! Using it is especially dangerous for GB simulation ! = 2 Andersen temperature coupling scheme. ! Depends on 'vrand' option ! = 3 Langevin dynamics with the collision frequency ! 'gamma_ln > 0'. In general case, gamma_ln=1.0 will ! produce a good result. temp0=310.0, ! Reference temperature at which the system is to be kept !tempi=0.0, ! Initial temperature. For the initial dynamics run ig=-1, ! The seed for the pseudo-random number generator. ! If ig=-1, the random seed will be based on the current ! date and time, and hence will be different for every run. ! ig=-1 with ntt=2, 3 is recommended. gamma_ln=1.0, ! The collision frequency in /ps, when ntt = 3. ! Default is 0 ! Pressure regulation ------------------------------------------------------- !ntp=0, ! Flag for constant pressure dynamics. This options should ! be set to 1 or 2 when Constant Pressure periodic boundary ! condition are used. ! = 0 No pressure scaling (Default) ! = 1 md with isotropic position scaling ! = 2 md with anisotropic pressure scaling: this should ! only be used with orghogonal boxes. ! = 3 md with semiisotropic pressure scaling: this is only ! available with constant surface tension (csurften > 0 ! ) and orthogonal boxes. barostat=2, ! Flag used to control which barostat to use in order to ! control the pressure. ! = 1 Berendsen (Default) ! = 2 Monte Carlo barostat (New in Amber 14, Faster) ! SHAKE bond length constraints --------------------------------------------- ntc=2, ! Flag for SHAKE to perform bond length constraints. ! =1 SHAKE is not performed (default) ! =2 bonds involving hydrogen are constrained ! =3 all bounds are constrained (not available for parallel ! or qmmm runs in sander) ! Since SHAKE is an algorithm based on dynamics, the ! minimizer is not aware of what SHAKE is doing, thus ! minimization generally should be carried out without it. ! Potential function parameters --------------------------------------------- ntf=2, ! Force evaluation. If SHAKE is used, it is not necessary ! to calculate forces for the constrained bonds (NTF=NTC) ! =1 complete interaction is calculated (default) ! =2 bond interactions involving H-atoms omitted (NTC=2) ! =3 all the bond interactions are omitted (NTC=3) ! See p. 295 Amber 14 for more options cut=9999.0, ! This is used to specify the nonbounded cutoff, in Ang. ! For PME, the cutoff is used to limit direct space sum, ! and 8.0 is usually a good value. When igb>0, the cutoff ! is used to truncate nonbounded pairs; here a larger value ! than the default is generally required (perhrps 16). ! When igb>0: the default is 9999.0 (effectively infinite) ! When igb=0: the default is 8.0 ! Generalized Born model parameters ----------------------------------------- igb=8, ! Flag for Generalized Born (GB) model simulation /