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input_all.toml
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title = "sis input"
[Job]
type = "MD"
# Aveilable options:
# "MD"
# "DCD"
# "CHECK_FORCE"
[Files]
[Files.In]
ff = "./rna_cg1_para2.ff"
# Force-field file. Required.
fasta = "./beta-globin.fasta"
# FASTA sequence file. Required unless [repeat] section is specified.
pdb_ini = "initial.pdb"
xyz_ini = "initial.xyz"
# File for initial structure. Only one of them is required.
# Only the coordinates will be read from these files,
# and any sequence information written will be ignored.
dcd = "./trajectory.dcd"
# DCD file to read. Required if type = "DCD" in [job].
anneal = "./annealing_schedule.txt"
# Annealing-schedule file.
# Required only when opt_anneal > 0 in [condition].
## Specific secondary structure.
## If either 'ct' or 'bpseq' is given, only base pairs that constitute
## the secondary structure are enabled.
ct = "./test.ct"
# CT (Connectivity Table) file
bpseq = "./test.bpseq"
# BPSEQ file (no comment line allowed)
[Files.Out]
prefix = "./test"
types = ["bp", "bpe", "bpall"]
[Condition]
tempK = 310.15
# Specify the simulation temperature in Kelvin.
# This line will be ignored if opt_anneal = 1.
rng_seed = 123
# (optional, but highly recommended to set)
# Seed value for the pseudorandom number generator.
# Set a 64-bit integer. If omitted, it will be set based on SYSTEM_CLOCK.
opt_anneal = 0
# (optional) flag for simulated annealing.
# 0: No annealing (default)
# 1: Annealing ("anneal" is required in [files.in])
temp_independent = 0
# (optional) temperature independent potential
# 0: Use the original (temperature-dependent) potential. (default)
# 1: Use temperature-independent potential. temp_ref is required.
tempK_ref = 328.15
[repeat]
n_repeat = 47
n_chain = 64
[PBC_box]
# (optional)
# If this section is given, periodic boundary condition is enabled.
x = 809.972
y = 809.972
z = 809.972
[MD]
integrator = "GJF-2GJ"
dt = 0.05
nstep = 500000
nstep_save = 500
nstep_save_rst = 500
neighbor_list_margin = 10.0
# (optional) default is 10.0
viscosity_Pas = 0.00001
# (optional) default is 0.00001
# Viscosity in Pascal Second used in Langevin dynamics.
stop_wall_time_hour = 47.9
# (optional) Set wall-clock time limit for the job.
# If a positive value is specified, the job will be terminated once the wall time
# reaches the limit value. A restart file (.rst) will be recorded.
# The unit is hour and can be any positive real number, e.g. 0.25 for 15 minutes.
# If the specified value is negative, no limit will be set.
# The default is -1 thus no time limit.
# It is recommended to set a slightly smaller value than the resource time allowed,
# e.g. 47.9 for 48-hour job.
fix_com_origin = 0
# (optional) Fix the translational motion of the molecule.
# 0 : No operation (default)
# 1 : Move the center of mass to the origin when output the coordinates.
# This should not be used if there are more than one chains.
[Basepair]
model = 1
# 1: The model by Nguyen, Hori, Thirumalai (2022) Nat. Chem.
# 2: (obsolete)
# 3: Same as 1 but not allowing isolated base pairs.
# 4: Base pair potential U0 is calcualted by dG values of the nearest neighbour model.
# 5: Base pair potential U0 is calcualted by dH and dS values of the nearest neighbour model.
min_loop_size = 3
# Minimum loop size allowed. The default value is 3 if this option is omitted.
# It is the number of nucleotides that must exist between a base pair.
# E.g., if min_loop_size = 3, then (i) and (i+4) can form a base pair, whereas (i) and (i+3) cannot.
max_bp_per_nt = -1
# Maximum number of base pairs simultaneously formed by one nucleotide.
# The default is -1 if this option is omitted.
# If max_bp_per_nt <= 0, no limitation is applied.
[Electrostatic]
# (optional)
# If this section is given, electrostatic interaction is enabled.
ionic_strength = 0.1
# Ionic strength of the monovalent-ions in molar units.
cutoff_type = 1
# How to specify the cutoff distance for electrostatic interactions.
# = 1: Distance-based.
# The cutoff will be specified as distance in Angstrom. (default)
# = 2: Multiple of the Debye length.
# The cutoff will be a factor to be multiplied by Debye length.
cutoff = 50.0
# Either diestance (cutoff_type = 1) or multiple (cutoff_type = 2),
# depending on the choice of cutoff_type.
no_charge = [1, 27]
# (optional) array of positive integeres.
# Particles having no charges.
length_per_charge = 4.38178046
# Paremeter in ion-condensation theory in Angstrom.
[Progress]
# (optional)
# If this section is given, progress information will be output to STDOUT.
step = 1000
[variable_box]
# (optional)
step = 1000
change_x = -1.0
change_y = -1.0
change_z = -1.0
[Stage]
# (optional)
sigma = 10.0
epsilon = 1.2