start_simulation.py

Runs classical MD simulation

usage: sphinx-build [-h] --conf CONF --top TOP [--node_grid NODE_GRID]
                    [--skin SKIN] [--output_prefix OUTPUT_PREFIX]
                    [--output_file OUTPUT_FILE] [--trj_collect TRJ_COLLECT]
                    [--energy_collect ENERGY_COLLECT]
                    [--topol_collect TOPOL_COLLECT] [--reactions REACTIONS]
                    [--debug DEBUG] [--check_topology CHECK_TOPOLOGY]
                    [--start_ar START_AR] [--stop_ar STOP_AR]
                    [--table_groups TABLE_GROUPS] [--max_force MAX_FORCE]
                    [--rate_arrhenius RATE_ARRHENIUS]
                    [--exclusion_list EXCLUSION_LIST]
                    [--benchmark_data BENCHMARK_DATA]
                    [--system_monitor_filter SYSTEM_MONITOR_FILTER]
                    [--do_not_exclude_bonds DO_NOT_EXCLUDE_BONDS] [--kb KB]
                    [--mass_factor MASS_FACTOR] [--run RUN]
                    [--int_step INT_STEP] [--rng_seed RNG_SEED]
                    [--thermal_groups THERMAL_GROUPS]
                    [--gen_velocity GEN_VELOCITY] [--thermostat {lv,vr,iso}]
                    [--barostat {lv,br}] [--barostat_tau BAROSTAT_TAU]
                    [--barostat_mass BAROSTAT_MASS]
                    [--barostat_gammaP BAROSTAT_GAMMAP]
                    [--thermostat_gamma THERMOSTAT_GAMMA]
                    [--temperature TEMPERATURE] [--pressure PRESSURE]
                    [--dt DT] [--lj_cutoff LJ_CUTOFF] [--cg_cutoff CG_CUTOFF]
                    [--coulomb_epsilon1 COULOMB_EPSILON1]
                    [--coulomb_epsilon2 COULOMB_EPSILON2]
                    [--coulomb_kappa COULOMB_KAPPA]
                    [--coulomb_cutoff COULOMB_CUTOFF]
                    [--store_species STORE_SPECIES]
                    [--store_state STORE_STATE]
                    [--store_position STORE_POSITION]
                    [--store_lambda STORE_LAMBDA] [--store_force STORE_FORCE]
                    [--store_velocity STORE_VELOCITY]
                    [--store_charge STORE_CHARGE] [--store_mass STORE_MASS]
                    [--store_res_id STORE_RES_ID]
                    [--store_pressure STORE_PRESSURE]
                    [--store_single_precision STORE_SINGLE_PRECISION]
                    [--save_before_reaction SAVE_BEFORE_REACTION]
                    [--trj_flush TRJ_FLUSH]
                    [--gro_trj_collect GRO_TRJ_COLLECT]
                    [--store_angdih STORE_ANGDIH]
                    [--maximum_conversion MAXIMUM_CONVERSION]
                    [--eq_steps EQ_STEPS] [--keep_simulation KEEP_SIMULATION]
                    [--count_types COUNT_TYPES] [--count_tuples COUNT_TUPLES]
                    [--count_types_state COUNT_TYPES_STATE]
                    [--count_fix_distances COUNT_FIX_DISTANCES]
                    [--t_hybrid_bond T_HYBRID_BOND]
                    [--t_hybrid_angle T_HYBRID_ANGLE]
                    [--t_hybrid_dihedral T_HYBRID_DIHEDRAL]

General options

--conf	Input .gro coordinate file
--top, --topology
	Topology file
--node_grid
--skin	Skin value for Verlet list Default: 0.16
--output_prefix
	Prefix for output files Default: “sim”
--output_file	Name of output trajectory file Default: “trjout.h5”
--trj_collect	Collect trajectory every (step) Default: 1000
--energy_collect
	Collect energy every (step) Default: 1000
--topol_collect
	Collect topology every (step) Default: 1000
--reactions	Configuration file with chemical reactions
--debug	Turn on logging mechanism
--check_topology
	If set to true then show the message generated by TopologyManager Default: False
--start_ar	When to start chemical reactions Default: 0
--stop_ar	When to stop chemical reactions Default: -1
--table_groups	The list of atom type names that should be simulated with tabulated potential.
--max_force	Maximum force in the system. Default: -1
--rate_arrhenius
	Change rate based on the Arrhenius equation. Default: False
--exclusion_list
	Read exclusion list from external file
--benchmark_data
	Store time measurement in the file
--system_monitor_filter
	Print all (empty) or only selected elements in SystemMonitor
--do_not_exclude_bonds
	Do not exclude newly created bonds Default: False

Simulation parameters

--kb	Boltzmann constant, default kJ/mol Default: 0.0083144621
--mass_factor	Mass units, default a.u. Default: 1.6605402
--run	Number of simulation steps Default: 10000
--int_step	Steps in integrator Default: 1000
--rng_seed	Seed for RNG Default: 7975
--thermal_groups
	Thermal groups
--gen_velocity	Generate velocity or not Default: False
--thermostat	Possible choices: lv, vr, iso Thermostat to use, lv: Langevine, vr: Stochastic velocity rescale Default: “lv”
--barostat	Possible choices: lv, br Barostat to use, lv: Langevine, br: Berendsen Default: “lv”
--barostat_tau	Tau parameter for Berendsen barostat Default: 5.0
--barostat_mass
	Mass parameter for Langevin barostat Default: 50.0
--barostat_gammaP
	gammaP parameter for Langevin barostat Default: 1.0
--thermostat_gamma
	Thermostat coupling constant Default: 5.0
--temperature	Temperature Default: 458.0
--pressure	Pressure
--dt	Integrator time step Default: 0.001
--lj_cutoff	Cutoff of atomistic non-bonded interactions Default: 1.2
--cg_cutoff	Cuoff of coarse-grained non-bonded interactions Default: 1.4
--coulomb_epsilon1
	Epsilon_1 for coulomb interactions Default: 1.0
--coulomb_epsilon2
	Epsilon_2 for coulomb interactions Default: 80.0
--coulomb_kappa
	Kappa paramter for coulomb interactions Default: 0.0
--coulomb_cutoff
	Coulomb cut-off Default: 0.9

H5MD storage

--store_species
	Store particle types Default: True
--store_state	Store chemical state Default: True
--store_position
	Store positions Default: True
--store_lambda	Store lambda parameter Default: False
--store_force	Store forces Default: False
--store_velocity
	Store velocity Default: False
--store_charge	Store charge Default: False
--store_mass	Store mass Default: True
--store_res_id	Store res_id Default: True
--store_pressure
	Compute and store pressure Default: False
--store_single_precision
	Write data in single precision format Default: True
--save_before_reaction
	If True then the trajectory and topology will be saved before reaction Default: False
--trj_flush	Flush data to disk every n-steps
--gro_trj_collect
	Save trajectory in .gro file
--store_angdih	Save angles and dihedrals in the topology Default: False

Maximum conversion

--maximum_conversion
	The comma separated list of conditions on which the simulation will stop. (format: atom type symbol(state):max number:total number)
--eq_steps	Run simulation after conversion reached for n-steps Default: 0
--keep_simulation
	Keep simulation running until the conversion is reached Default: False

Counters

--count_types	List of particle types to count; eq. A,B
--count_tuples	Count tuples Default: False
--count_types_state
	List of particle types, state; eq. A:3,B:4
--count_fix_distances
	Count size of fix distances Default: False

Hybrid bonded terms

--t_hybrid_bond
	Use hybrid bonds Default: 0
--t_hybrid_angle
	Use hybrid angles Default: 0
--t_hybrid_dihedral
	Use hybrid dihedrals Default: 0