From c73b436d0342aa130e1e3beb3d0b241e8f3c18bd Mon Sep 17 00:00:00 2001 From: Samiran Sen Date: Mon, 8 Nov 2021 11:41:05 +0100 Subject: [PATCH] Add HyMD inputs lipidA --- examples/lipidA.toml | 118 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 118 insertions(+) create mode 100644 examples/lipidA.toml diff --git a/examples/lipidA.toml b/examples/lipidA.toml new file mode 100644 index 00000000..7e2605da --- /dev/null +++ b/examples/lipidA.toml @@ -0,0 +1,118 @@ +[meta] +# Name of the simulation. May be ommitted. +name = "LipidA with Ca2+ in solution" +# Tags classifying the simulation. May be ommitted. +tags = ["vesicle", "solvent", "LipidA"] + +[particles] +# Number of total particles in the simulation. If an input .hdf5 format file is +# specified, the number of particles will be inferred from this and *may* be +# ommited. +n_particles = 71318 +# Mass of the particles in [g/mol]. All masses are assumed equal. +mass = 72.0 +# Maximum number of particles per molecules present in the system. A default of +# 200 is assumed, and this keyword may be ommitted for any system with smaller +# molecules. +max_molecule_size = 30 + +[simulation] +# Number of total time steps in the simulation. +n_steps = 3 +# Frequency of trajectory/energy file output in time steps. +n_print = 1 +# Frequency of requesting that the HDF5 library flush the file output buffers +# to disk after in number of n_print timesteps. +n_flush = 1 +# Time step used in the simulation in [picoseconds]. +time_step = 0.3 +# Simulation box size in [nanometers]. +box_size = [20.0, 20.0, 20.0] +# Time integrator used in the simulation. Either "velocity-verlet" or "respa". +# If "respa", specify also the number of small rRESPA time steps per large +# time_step with the 'respa_inner' keyword. +integrator = "respa" +respa_inner = 10 +# Perform MPI rank domain decomposition every x time steps to (hopefully) +# reduce the amount of neccessary communication between ranks in the pmesh +# procedures. Ommit or set to 'false' or '0' to not perform any domain +# decomposition. +domain_decomposition = 50000 +# Remove linear center of mass momentum from the system before integration +# starts and at every x steps subsequently. If 'true', the linear momentum is +# removed before starting. Ommit or set to 'false' or 0 to never remove the +# center of mass momentum. +cancel_com_momentum = 20 +# Starting temperature to generate before simulation begins in [kelvin]. Ommit +# or set to 'false' to not change the temperature before starting. +start_temperature = 323 +# Target temperature used in the velocity rescale thermostat in [kelvin]. Ommit +# or set to 'false' to use no thermostat, i.e. a constant energy simulation. +target_temperature = 323 +# Thermostat collision frequency in [1/picoseconds]. +tau = 0.7 +# Couple groups of particles species to individual different thermostats. +thermostat_coupling_groups = [ + ["P", "G", "L", "C"], + ["W"], + ["CA"] +] +# The energy functional W[phi] to use. Options: +# "SquaredPhi": φ² / 2κφ₀, +# "DefaultNoChi": (φ - φ₀)² / 2κφ₀ +# "DefaultWithChi": (φ - φ₀)² / 2κφ₀ + Σ χφφ' / φ₀ +# Subclass Hamiltonian to create a new energy functional. +hamiltonian = 'DefaultNoChi' + + +[field] +# Particle-mesh grid size, either a single integer or an array of 3 integers +# (number of grid points in each dimension). In order to guarantee consistency +# and speed in the PFFT routines, the actual mesh grid will be changed to ensure +# that each dimension of the 2d PFFT process grid divides each dimension of the +# mesh grid size. +mesh_size = [24, 24, 24] +# Compressibility used in the relaxed incompressibility term of W(phi) in +# [mol/kJ]. +kappa = 0.05 +# Standard deviation in the Gaussian filter (window function) in [nanometers]. +# This value is a characteristic length scale for the size of the particles in +# the simulation. +sigma = 0.5 +# Electrostatics +coulombtype = 'PIC_Spectral' +dielectric_const = 20.0 +# Interaction matrix, chi, ((atom name 1, atom name 2), (mixing energy in +# [kJ/mol])). +chi = [ + [["L", "G"], [4.5]], + [["L", "C"], [13.25]], + [["P", "G"], [4.5]], + [["P", "C"], [20]], + [["P", "CA"], [-7.2]], + [["P", "W"], [-3.6]], + [["G", "C"], [8.3]], + [["G", "W"], [4.5]], + [["C", "CA"], [13.25]], + [["C", "W"], [33.75]], +] + +[bonds] +# Two-particle bonds, ((atom name 1, atom name 2), (equilibrium length in +# [nanometers], bond strength in [kJ/mol])). Note the two +bonds = [ + [["L", "G"], [0.47, 1250.0]], + [["L", "C"], [0.47, 1250.0]], + [["G", "P"], [0.37, 1250.0]], + [["G", "G"], [0.47, 1000.0]], + [["G", "C"], [0.47, 1250.0]], + [["C", "C"], [0.47, 1250.0]], +] +# Three-particle angular bonds, ((atom name 1, atom name 2, atom name 3), +# (equilibrium angle in [degrees], bond strength in [kJ/mol])). +angle_bonds = [ + [["G", "G", "G"], [120.0, 850.0]], + [["G", "G", "L"], [120.0, 25.0]], + [["L", "C", "C"], [180.0, 25.0]], + [["C", "C", "C"], [180.0, 25.0]], +]