# Simulation box settings, as well as the parameters detailing simulation-box-
# related simulation protocols, such as squeezing, oscillations etc.
simulation box:
# Initial size specification.
initial size:
# Type of the derivation of the initial simulation box size. Options:
# - "sufficient": the box is such as to contain all the residues. See
# `sufficient box params` for more details.
# - "from CRYST1 record": the box is set to one spanning from [0, 0, 0] to
# [a, b, c] where the latter values are taken from CRYST1 record in the
# PDB file. Note: this usually only makes sense if the periodic boundary
# conditions are enabled, or there are no walls.
# - "keep from SAW": the box is set to one which was used in the SAW
# procedure with the periodic boundary conditions (Note: this is **not**
# the same as the CRYST1 box, as the latter is not actually used in the
# SAW procedure, even if periodic boundary conditions are used)
# - "infinite": the simulation box is boundless; of course, this setting
# only makes sense with no walls.
type: sufficient
# Further parameters for the "sufficient" option for the "type" property
# above.
sufficient box params:
# A multiple of the bond size (derived as mentioned previously), which
# gets added in each direction to the minimal box containing the residues.
pad (x bond): 2.0
# Maximum density of the box. Optional. To be more specific, if set, the
# simulation box necessarily contains a cube with a size derived so as to
# make it have the specified molar density, in a fashion similar to an
# option "start box" in the section about morphing into SAW, centered in
# zero.
maximum density: 1e-4 residue/A**3
# Whether the generated simulation box should be cubic or not.
cubic: false
# Parameters for the simulation box walls.
walls:
# Types of the walls. This can be set separately for x/y/z axes, as well as
# set for all axes at the same time.
# The key options are:
# - "x axis", "y axis", "z axis": separately;
# - "all axes": all at once.
# The wall types are:
# - "void": no walls on the given axis/axes;
# - "periodic": periodic boundary conditions on a given
# axis/axes (this is, one must admit, a mild misuse of the language, but
# putting it here seems like a most fitting option.)
# - "solid": the walls being "solid", i.e. described by potential V ~ d^{-9}.
# Note that, if enabled, the walls can change the type to an attractive one
# during the simulation; this usually only makes sense if the type of the
# wall is "solid".
all axes: void
# Threshold for the wall interactions. (Note: equivalent to `walmindist`)
threshold: 5.0 A
# Parameters for the "solid" wall type.
solid wall params:
# Depth of the potential.
depth: 4.0 eps
# Parameters for the LJ attractive wall type.
lj wall params:
# Depth of the potential.
depth: 4.0 eps
# Timespan, over which the target depth is acquired quasi-adiabatically.
cycle duration: 0.0 tau
# A multiplier for the minimum of the radius, above which the connection
# of a residue with the wall is considered to be broken.
breaking dist factor: 1.5
# Connection limit for each wall.
# Options:
# - a number: a fixed number of connections.
# - "auto": a value derived via a fairly complex formula which I won't
# reproduce here.
connection limit: auto
# Parameters for the harmonic attractive wall type.
harmonic wall params:
# The "depth": V = HH1 d^2
HH1: 30.0 eps/A**2
# Connection limit for each wall. See the description in the
# "lj wlal params" for details.
connection limit: auto
# Common parameters for squeezing, oscillations etc.
common:
# A "resting period" between various phases of the simulation.
rest period: 10e3 tau
# Maximum (regular) velocity of wall movement, reached with constant
# acceleration over a given distance.
target velocity: 5e-3 A/tau
# Distance, over which the walls reach the full/target velocity.
distance before acquiring full velocity: 12.0 A
# A span of time, over which to average the wall forces. The value of this
# force average is not computed with relation to the current time point -
# rather, simulation is divided into "time windows", and the current value of
# the force average is equal to the average of forces in the *previous* window;
# in the first window, the value is undefined.
average forces over: 100 tau
# Squeezing phase settings.
squeezing:
# Whether to perform box squeezing.
perform: false
# Density of the target box.
target density: 1e-3 residue/A**3
# Velocity used when the simulation box volume is twice above the target
# volume - this being done to speed up the simulation, as one presumes that
# one needs not be that careful when there are barely any residues
# interacting with the walls.
velocity above 2V: 2e-2 A/tau
# "Finding force minimum" phase.
finding force minimum:
# Whether to perform the phase.
perform: false
# Force for max velocity. The velocity of the wall is proportional to the
# forces acting on the wall, clipped at a given force threshold.
force for max velocity: 0.4 eps/A
# Oscillations phase.
oscillations:
# Whether to perform the phase.
perform: false
# Type of wall movement. Options:
# - "squeeze": in which the z-axis walls are moved closer/apart.
# - "shear": in which the z-axis walls are moved along the x-axis.
type: squeeze
# Number of oscillation cycles to perform.
num of cycles: 6
# Parameters for the amplitude of the oscillations.
amplitude:
# Variant of the derivation of the amplitude. Options:
# - "absolute": the amplitude value is as given in "absolute value" entry
# below;
# - "relative": the amplitude value is the distance between the z-axis
# walls multiplied by the value of "relative value" entry below.
variant: absolute
absolute value: 10.0 A
relative value: 0.1
# Angular frequency of the oscillations.
angular frequency: 1e-4 rad/tau
# "Pulling at the end" phase. [Not implemented]
pulling at the end:
# Whether to perform the phase.
perform: false
# Parameters for attractive walls. [Not implemented]
attractive walls:
# When to turn on the attractive walls. Options: ??
when: never
# Type of attractive wall: Options: "lj", "harmonic".
type: lj