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Example

command_name: type->default

※※※※※

Type items:

English name	Chinese name	Notes
float	Floating-point number	Basic type
int	Integer	Basic type
string	String	Basic type
enum	Option	See each command for available values
bool	Boolean	0 or 1
file	File name	File paths should not contain spaces
CV	CV	CV defined by cv_in_file
【type1】【symbol】【type2】	【type1】 and 【type2】 separated by 【symbol】	Example: “int int” means two integers separated by a space
[【type】]	A sequence of 【type】 values separated by spaces	Example: “[int]” means a sequence of integers
【type】【symbol】…【symbol】【type】	A sequence of 【type】 values separated by 【symbol】	Example: “float/…/float” means a sequence of floating-point numbers separated by ”/”

The number of ※ marks indicates how often the command needs to be set.

Number of ※	Setting frequency
※	Set during development and testing
※※	Rarely set during use
※※※	Set according to the system during use
※※※※	Frequently set during use
※※※※※	Usually set during use

MD Core

System Information

mdin: file->mdin.txt

※※※※※ Command-control input file

cv_in_file: file

※※※ CV-control input file

pbc: bool->1

※※※ Whether to enable periodic boundary conditions

mode: enum

※※※※※ Run mode

Available value	Meaning
NVE	NVE ensemble simulation
NVT	NVT ensemble simulation
NPT	NPT ensemble simulation
minimization	Energy minimization
rerun	Rerun a trajectory

dt: float->1e-3(non-minimization); 1e-8(minimization)

※※※※※ Time step [ps], available only in non-rerun modes

step_limit: int->1000

※※※※※ Total number of simulation steps, available only in non-rerun modes

thermostat: enum

※※※※※ Thermostat method, available only in NVT and NPT modes See Modules for available values

target_temperature: float->300.0

※※※※ Ensemble temperature [K], available only in NVT and NPT modes

barostat: enum

※※※※※ Barostat method, available only in NPT mode See Modules for available values

target_pressure: float->1.0

※※※※ Ensemble pressure [bar], available only in NPT mode

velocity_max: float->-1

※※※ Maximum particle velocity [22.45 Angstrom/ps]. This prevents a particle with an accidentally excessive velocity from crashing the system. Negative values disable the check.

If this needs to be set, a reference value at 300 K is 20.

default_in_file_prefix: string

※※※※※ After this is defined, xxx_in_file automatically looks for the corresponding file. For example, coordinate_in_file automatically looks for default_in_file_prefix_coordinate.txt.

coordinate_in_file: file

※※※※※ Coordinate input file

velocity_in_file: file

※※※※ Velocity input file

mass_in_file: file

※※ Mass input file

charge_in_file: file

※※ Charge input file

residue_in_file: file

※※ Residue input file

end_pause: bool->0

※※ Whether an extra Enter key press is required when the program ends

device: int->0

※※※ GPU device index to use

dont_check_input: bool->0

※※ Do not print warnings generated by the input

Suppressing warnings is dangerous. Make sure you understand what these warnings mean.

AMBER Compatibility

AMBER files were used only in early testing and were retained afterward. In later feature implementations, many functions no longer support reading AMBER-format files.

amber_parm7: file

※※ AMBER-format topology input file

amber_rst7: file

※※ AMBER-format coordinate input file

amber_irest: bool->1

※ Parameter for the AMBER-format coordinate input file. The following logic determines whether the file contains velocity information:

• If set to 0, there is no velocity information.
• If set to 1:
  • If amber_rst7 does not contain time information, there is no velocity information.
  • If amber_rst7 contains time information, velocity information is present.

Output Information

make_output_whole: [int-int]

※※※ Map the atom pairs defined by make_output_whole into the same periodic boundary when outputting trajectories

write_information_interval: int->1000

※※※※ Output the trajectory every write_information_interval steps

write_mdout_interval: int->write_information_interval

※※※ Output an mdout file every write_mdout_interval steps

write_restart_file_interval: int->step_limit

※※※ Output a restart file every write_restart_file_interval steps

crd: file->mdcrd.dat

※※※ Trajectory file

box: file->mdbox.txt

※※※ Box trajectory file

rst: string->restart

※※※

• If the initial coordinates are provided through amber_rst7, this is the output restart file name.
• If the initial coordinates are provided through coordinate_in_file, this is the output restart file prefix.

frc: file

※※※ Force trajectory file

vel: file

※※※ Velocity trajectory file

Trajectory Rerun

frame_limit: int

※※※ Total number of rerun steps

rerun_start: int->0

※※※ In rerun mode, start reading the trajectory file after frame rerun_start

rerun_strip: int->0

※※※ In rerun mode, skip rerun_strip frames each time the trajectory is read after the start

Nonbonded Information

skin: float->2.0

※※ Nonbonded “skin” thickness [Angstrom]. When any atom moves more than skin * skin_permit, the neighbor list is updated. The neighbor list contains particles within skin + cutoff around each atom.

cutoff: float->10.0

※※※※※ Nonbonded cutoff distance [Angstrom]

The default parameter of 10.0 Angstrom is too small for simulations under non-periodic boundary conditions.

exclude_in_file: file

※※ Nonbonded exclusion-list input file

Neighbor List

neighbor_list_refresh_interval: int->0

※※※ Neighbor-list update interval in steps. If this is not positive, the list is updated automatically after any atom moves more than skin * neighbor_list_skin_permit.

neighbor_list_max_atom_in_grid_numbers: int->80

※※ Maximum number of atoms in each neighbor-list grid cell, used for memory allocation

neighbor_list_max_neighbor_numbers: int->1200

※※ Maximum number of neighbors per atom, used for memory allocation

neighbor_list_skin_permit: float->0.5

※※※ In the automatic neighbor-list update logic, the allowed fraction of skin that atoms may move. When neighbor_list_skin_permit = 0.5, the result is accurate; larger values are faster but slightly reduce accuracy.

PME

PME_update_interval: int->1

※※※ Setting parameter for multiple-time-step updates. The PME long-range part is updated once every PME_Update_Interval steps.

PME_print_detail: bool->0

※※ Print detailed results for each PME component

PME_replaced_by_PMC_IZ: bool->0

※※※ Use PMC_IZ instead of PME for calculation

PME_fftx: int->nearest number close to a multiple of 4 selected at 1 Angstrom per grid point

※※ Number of grid points for the Fourier transform in the x direction

PME_ffty: int->nearest number close to a multiple of 4 selected at 1 Angstrom per grid point

※※ Number of grid points for the Fourier transform in the y direction

PME_fftz: int->nearest number close to a multiple of 4 selected at 1 Angstrom per grid point

※※ Number of grid points for the Fourier transform in the z direction

PME_Direct_Tolerance: float->1e-5

※※ Error [kcal/mol] from hard cutoff at cutoff in the direct part between two unit point charges

PME_calculate_reciprocal_part: bool->1

※ Whether to calculate the reciprocal-space part of PME

calculate_excluded_part: bool->1

※ Whether to calculate the exclusion-list part of PME

Energy Minimization

minimization_max_move: float->0.1

※※※ Maximum movement distance per step [Angstrom]

minimization_momentum_keep: float->0

※※※ Fraction of momentum retained at each minimization step

minimization_dynamic_dt: int->1

※※ Whether to use a dynamic time step. 1 enables it, and 0 disables it.

minimization_dt_decreasing_rate: float->0.01

※※ Decrease parameter when the time step changes dynamically

minimization_dt_increasing_rate: float->1.01 + random number from 0 to 1

※※ Increase parameter when the time step changes dynamically

minimization_dt_factor: float->1e-4 + 1e-2 * random number from 0 to 1

※※※ dt factor when the time step changes dynamically

Thermostat

andersen_thermostat_update_interval: int->500

※※※※ Randomly generate velocities every andersen_thermostat_update_interval steps

andersen_thermostat_seed: int->time

※ Random number seed

berendsen_thermostat_tau: float->1.0

※※※※ Time parameter [ps]

berendsen_thermostat_stochastic_term: bool->0

※※※ Whether to enable stochastic correction

berendsen_thermostat_seed: int->time

※ Random number seed used for stochastic correction

nose_hoover_chain_length: int->1

※※※※ Chain length

nose_hoover_chain_tau: float->1.0

※※※※ Time constant [ps]

nose_hoover_chain_restart_input: file

※※ Initial velocities and coordinates of the extended dimensions

nose_hoover_chain_restart_output: file

※※ Final velocities and coordinates of the extended dimensions

nose_hoover_chain_crd: file

※※ Coordinate trajectory of the extended dimensions

nose_hoover_chain_vel: file

※※※ Velocity trajectory of the extended dimensions

middle_langevin_gamma: float->1.0

※※※※ Friction factor [ps−1\rm ps^{-1}ps−1]

middle_langevin_seed: int->random integer

※ Random number seed

langevin_gamma: float->1.0

※※※※ Friction factor [ps−1\rm ps^{-1}ps−1]

langevin_seed: int->random integer

※ Random number seed

Barostat

monte_carlo_barostat_initial_ratio: float->0.001

※※ Initial change in each side length as a fraction of the initial side length

monte_carlo_barostat_update_interval: int->100

※※ Attempt one volume change every monte_carlo_barostat_update_interval steps

monte_carlo_barostat_check_interval: int->100

※※ Check parameters every monte_carlo_barostat_check_interval steps

monte_carlo_barostat_molecule_scale: bool->1

※※ Whether to control pressure by scaling whole molecules or by scaling atoms

If this is set to 0 while a constraint algorithm is used, abnormal behavior may occur, causing the system to crash or the volume to never reach equilibrium.

monte_carlo_barostat_accept_rate_low: float->30

※※ During checks, ensure that the Monte Carlo acceptance rate is at least monte_carlo_barostat_accept_rate_low %

monte_carlo_barostat_accept_rate_high: float->40

※※ During checks, ensure that the Monte Carlo acceptance rate is at most monte_carlo_barostat_accept_rate_high %

monte_carlo_barostat_couple_dimension: enum->XYZ

※※※ Coupling of the volume-control directions in Monte Carlo barostatting

Available value	Meaning
XYZ	Isotropic
NO	Anisotropic
XY	X and Y directions are coupled; Z direction is independent
XZ	X and Z directions are coupled; Y direction is independent
YZ	Y and Z directions are coupled; X direction is independent

monte_carlo_barostat_only_direction: enum

※※※ Change only one dimension during a Monte Carlo move

Available value	Available value
X	XY
Y	XZ
Z	YZ

You cannot perform an invalid operation, such as requiring XYZ coupling while changing only the X dimension.

monte_carlo_barostat_surface_number: int->0

※※※ Number of interfaces in the system

monte_carlo_barostat_surface_tension: float->0

※※※ Surface tension [mN/m]

berendsen_barostat_tau: float->1.0

※※※※ Time constant [ps]

berendsen_barostat_compressibility: float->4.5e-5

※※ Compressibility [bar−1\rm bar^{-1}bar−1]

berendsen_barostat_stochastic_term: bool->0

※※※ Whether to add stochastic correction

berendsen_barostat_update_interval: int->10 (without stochastic correction); 1 (with stochastic correction)

※※ Control pressure once every berendsen_barostat_update_interval steps

berendsen_barostat_seed: int->time

※ Random number seed for stochastic correction

andersen_barostat_tau: float->1.0

※※※※ Time constant [ps]

andersen_barostat_compressibility: float->4.5e-5

※※ Compressibility [bar−1\rm bar^{-1}bar−1]

andersen_barostat_dV_dt: float->0

※※※ Initial rate of volume change [20.455 A˚3/fs\rm 20.455\ Å^3/fs20.455 A˚3/fs]

Force Field

See File Formats for force-field file formats.

See the Modules page for force-field forms.

bond_in_file: file

※※ Harmonic bond length

bond_soft_in_file: file

※※ Soft bond

angle_in_file: file

※※ Harmonic bond angle

urey_bradley_in_file: file

※※ Urey_Bradley bond angle

dihedral_in_file: file

※※ Periodic dihedral angle

improper_in_file: file

※※ Harmonic dihedral angle

nb14_in_file: file

Modified LJ and modified electrostatic 1-4 interactions

nb14_extra_in_file: file

※※ Independent LJ parameters and modified electrostatic 1-4 interactions

cmap_in_file: file

※※ CMAP force field

LJ_in_file: file

※※ LJ force field

vatom_in_file: file

※※ Virtual-atom force field

gb_in_file: file

Used only under non-periodic boundary conditions.

※※ Simplest implicit-solvent force field

listed_forces_in_file: file

※※ Custom bonded-interaction force field

pairwise_force_in_file: file

※※ Custom nonbonded-interaction force field

Restraints and Constraints

restrain_atom_id: file

※※※ Atom serial numbers for positional restraints

You can use the maskgen function in Xponge to call MDAnalysis and generate this file. See Xponge maskgen -h for details.

restrain_coordinate_in_file: file

※※※ Reference coordinates for positional restraints

restrain_amber_rst7: file

※※ Reference coordinates for positional restraints in AMBER format

restrain_weight: float->20.0

※※※ Force constant for positional restraints [kcal/mol/A2\rm kcal/mol/A^2kcal/mol/A2]

constrain_mode: enum

※※※※ Constraint mode

Available value	Meaning
shake	SHAKE algorithm
simple_constrain	Simple constraint algorithm

constrain_mass: float->3.3(if constrain_in_file is not given);0(if constrain_in_file is given)

※※ Bonds involving atoms whose mass is less than constrain_mass are constrained

constrain_in_file: file

※※ File that explicitly specifies the bond lengths to constrain

In most cases, this file does not need to be provided, because the program automatically generates it according to constrain_mass.

constrain_angle: bool->0

※ Whether to constrain bond angles involving atoms whose mass is less than constrain_mass

After this is enabled, constraints may become difficult to converge for complex systems, and constraining bond angles is not physical. Enabling this is not recommended.

settle_disable: bool->0

※ Whether to disable SETTLE

simple_constrain_iteration_numbers: int->25

※ Number of iterations for the simple constraint algorithm

simple_constrain_step_length: float->1

※ Iteration step length for the simple constraint algorithm

shake_iteration_numbers: int->25

※ Number of iterations for the SHAKE constraint algorithm

shake_step_length: float->1

※ Iteration step length for the SHAKE constraint algorithm

Walls

hard_wall_x_low: float

※※※ When the x-coordinate component of a particle is less than this value, its velocity in the x direction becomes positive

hard_wall_x_high: float

※※※ When the x-coordinate component of a particle is greater than this value, its velocity in the x direction becomes negative

hard_wall_y_low: float

※※※ When the y-coordinate component of a particle is less than this value, its velocity in the y direction becomes positive

hard_wall_y_high: float

※※※ When the y-coordinate component of a particle is greater than this value, its velocity in the y direction becomes negative

hard_wall_z_low: float

※※※ When the z-coordinate component of a particle is less than this value, its velocity in the z direction becomes positive

hard_wall_z_high: float

※※※ When the z-coordinate component of a particle is greater than this value, its velocity in the z direction becomes negative

soft_walls_in_file: file

※※※ File that defines soft-wall potential functions

Selective Integrated Tempering Sampling

SITS_mode: enume

※※※ Mode

Available value	Meaning
observation	Observation mode
iteration	Iteration mode
production	Production mode

SITS_atom_in_file: file

※※※ File list of atoms to enhance. This command invalidates SITS_atom_numbers.

SITS_atom_numbers: int

※※※ The atoms to enhance are the first SITS_atom_numbers atoms in the system. This command is invalid when the SITS_atom_in_file command is in effect.

SITS_cross_enhance_factor: float->0.5

※※※ Enhancement factor for the AB cross term

SITS_dihedral_in_file: file

※※※ Dihedral angles requiring enhanced sampling, in the same format as a normal dihedral_in_file

---

The following commands are enabled only when SITS_mode is not observation.

---

SITS_k_numbers: int->40

※※※ Number of temperature partitions

SITS_T_high: float

※※※ Upper interval of temperature integration. Temperature grid points are obtained automatically by linear interpolation using SITS_k_numbers, SITS_T_high, and SITS_T_low.

SITS_T_low: float

※※※ Lower interval of temperature integration. Temperature grid points are obtained automatically by linear interpolation using SITS_k_numbers, SITS_T_high, and SITS_T_low.

SITS_T: float/../float

※※ Temperature grid points. This command is invalidated by SITS_T_high and SITS_T_low.

SITS_record_interval: int->1

※ Record energy every SITS_record_interval steps

SITS_update_interval: int->100

※ Update the bias-energy parameters every SITS_update_interval records

SITS_pe_a: float->1

※※※ Multiplier factor used when recording energy

SITS_pe_b: float->0

※※※ Translation parameter used when recording energy [kcal/mol]

SITS_fb_bias: float->0

※※ Final translation factor of fb

SITS_nk_rest: bool->0(iteration mode);1(production mode)

※ Whether to reread nk parameters

SITS_nk_in_file: file

※※※ File for rereading nk parameters

SITS_nk_fix: bool->0(iteration mode);1(production mode)

※ Whether nk parameters are fixed

---

The following commands are enabled only when SITS_nk_fix is 0.

---

SITS_nk_rest_file: file->SITS_nk_rest_file

※※※ nk restart file

SITS_nk_traj_file: file->SITS_nk_traj.dat

※※※ nk trajectory file