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input_all.toml
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title = "sis input"
[Job]
type = "MD"
# Available options:
# "MD": Default.
# "DCD": Read an existing DCD file (specified by [Files.In] dcd) and calculate energies.
# "CHECK_FORCE": For debug. Check consistency between the energy and force routines.
[Files]
[Files.In]
ff = "./rna_cg1_para2.ff"
# Force-field file. Required.
fasta = "./beta-globin.fasta"
# FASTA sequence file. Required.
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 therein will be ignored.
dcd = "./trajectory.dcd"
# DCD file to read. Required only if type = "DCD" in [Job].
anneal = "./annealing_schedule.txt"
# Annealing-schedule file.
# Required only when opt_anneal > 0 in [Condition].
bias_Rg = "./bias_Rg_schedule.txt"
# Schedule file for bias_Rg.
# Required only when potential = 'timed-flat-bottomed' in [Bias_Rg].
restraint = "./restraint.txt"
# Restraint file containing a list of pre-defined restraints.
## 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)
bpl = "./test.bpl"
# Basepair list file (no comment line allowed)
[Files.Out]
prefix = "./test"
types = ["bpcoef", "bp", "bpe", "bpall", "twz"]
# Available options:
# "bpcoef": bp parameters will be written.
# "bp": bp energy trajectory in binary format.
# "bpe": bp energy trajecotry in ASCII format.
# "twz": information of tweezers (force values for Force_Ramp)
[Molecules]
# (optional)
# This [Molecules] block is required unless the system contains only linear RNA chains.
# If this block is omitted, the number of chains is set equal to the number of chains
# in the FASTA file and all chains are assumed to be linear RNA.
n_chain = 2
1 = 'linearRNA' # default
2 = 'circRNA'
[Replica]
nrep_temp = 8
nrep_force = 0
nrep_ion = 0
nrep_rg = 0
nstep_exchange = 10
nstep_save = 100
## Perform exchange? (true (default) or false)
exchange = true
[Replica.Temperature]
1 = 293.15
2 = 303.15
3 = 313.15
4 = 323.15
5 = 333.15
6 = 343.15
7 = 353.15
8 = 363.15
[Replica.Force]
## External force using Tweezers.Dual_Constant_Force
1 = 0.0
2 = 2.0
3 = 4.0
4 = 6.0
5 = 8.0
6 = 10.0
7 = 12.0
8 = 14.0
[Replica.Ionic_strength]
## Ionic strength of the monovalent ions in molar (mol/L) units.
1 = 0.02
2 = 0.05
3 = 0.10
4 = 0.15
5 = 0.20
6 = 0.30
7 = 0.50
8 = 0.80
[Replica.Rg]
## Rg in Angstrom. [Bias_Rg] is required when nrep_rg > 1.
1 = 10.0
2 = 12.0
3 = 14.0
4 = 16.0
5 = 18.0
6 = 20.0
7 = 22.0
8 = 24.0
[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
[MD]
integrator = "GJF-2GJ"
# GJF-2GJ: Langevin dynamics using GJF-2GJ thermostat
# L.F.G. Jensen, N. Grønbech-Jensen (2019) Mol. Phys. DOI:10.1080/00268976.2019.1570369
# Ermak-McCammon: Brownian dynamics
# D.L. Ermak, J.A. McCammon (1978) J. Chem. Phys. DOI:10.1063/1.436761
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, default: -1) Wall-clock time limit for the job.
# The default is -1 thus no time limit.
# 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 generated at the time.
# 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.
# It is recommended to set a slightly smaller value than the resource time allowed,
# Since it may take some time for the program to exit normally, such as when saving files,
# it is recommended that you specify a slightly smaller value, e.g. 47.9 for 48-hour job.
nstep_check_stop = 10000
# (optional, default: 10000) Frequency to check the wall time to stop.
# The value has to be a positive integer. If a value less than 1 is specified,
# then nstep_check_stop = 1 will be used (check evey step).
# The simulation can also be stopped by placing an empty file named STOP_SIS at the same directory
# specified in [Files.In] prefix.
# e.g. if prefix = "./output/md", either ./output/stop_sis or ./output/STOP_SIS will terminate the 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 = 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 = 3, then (i) and (i+4) can form a base pair, whereas (i) and (i+3) cannot.
nstep_MC = 1
# (optional) default is 1.
# This variable specifies the frequency of Monte Carlo reorganisation of the base pair network.
# The value has to be 0 or any positive integer. If nstep_MC = 0, there will be no MC procedure.
# If [Job] type = "DCD", any positive integer value of nstep_MC will be ignored and MC will be
# performed for every frame (i.e. nstep_MC = 1). nstep_MC = 0 is still valid and MC will not be conducted.
max_bp_per_nt = 1
# (optional) default is 1
# Maximum number of base pairs simultaneously formed by one nucleotide.
# The value has to be positive integer. Only valid when nstep_MC > 0.
[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 distance (cutoff_type = 1) or multiple (cutoff_type = 2),
# depending on the choice of cutoff_type.
dummy_has_charge = false
# (optional) default is false
# If true, dummy particles (D) will have the same charge as normal RNA particles.
# These charges can be individually disabled by the 'no_charge' option below.
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.
exclude_covalent_bond_pairs = true
# If true, no electrostatic interaction between covalent-bond pairs (i)-(i+1). (default true)
#exclude_covalent_angle_pairs = true
# # If true, no electrostatic interaction between covalent-angle pairs (i)-(i+3). (default false)
[Progress]
# (optional)
# If this section is given, progress information will be output to STDOUT.
step = 1000000
[PBC_box]
# (optional)
# If this section is given, the Periodic Boundary Condition (PBC) is enabled.
size = [809.972, 809,972, 809.972]
#x = 809.972
#y = 809.972
#z = 809.972
# These 'x=', 'y=', 'z=' are an older way to specify the box size,
# which is deprecated and will be removed in a future version.
# Use size =[x, y, z] format.
resize_change = [ -0.1, -0.1, -0.1]
resize_target = [500.0, 500.0, 500.0]
resize_step = 1000
[Variable_box]
# This option is deprecated and will be removed in a future version.
# Use [PBC_box] resize_step, resize_change, and resize_target for the feature.
step = 1000
change_x = -1.0
change_y = -1.0
change_z = -1.0
[Stage]
# (optional)
# Stage potential
sigma = 10.0
epsilon = 1.2
[Freeze]
id_ranges = [[1, 5], [10,14]]
[Tweezers]
[Tweezers.Dual_Constant_Force]
id_pairs = [[1, 5],]
forces_pN = [[5.0, 0.0, 0.0],] # in pN
[Tweezers.Force_Ramp]
id_pairs = [[1, 27]]
spring_const = [[0.0030, 0.0030],] # in kcal/mol/(angstrom^2)
trap_speed = [[0.0, 1.5e-6]] # in angstrom per step
## In the Force_Ramp mode, a pair of particles (i, j) is specified by id_pairs = [[i, j],].
## The two particles are each trapped by tweezers with spring constants k_i and k_j
## specified by spring_const = [[k_i, k_j],]. The positions of the two traps are initially
## located at the same position as the particles i and j at time = 0 (xyz_i(0) and xyz_j(0)).
## The trap positions move along the simulation at the speed given by trap_speed = [[v_i, v_j],].
## The direction of movement is determined by the initial positions and is (xyz_j(0) - xyz_i(0)),
## i.e. the direction from xyz_i(0) to xyz_j(0).
## 'twz' output file will contain informaion of the extension and forces.
[Bias_SS]
force_pN = 20.0
[Bias_Rg]
potential = 'harmonic'
#potential = 'flat-bottomed'
#potential = 'timed-flat-bottomed'
k = 1.0
Rg0 = 12.0