BioSimSpace.Protocol.ATMEquilibration

class BioSimSpace.Protocol.ATMEquilibration(system=None, data=None, timestep=2.0000 fs, runtime=0.2000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=1.0000 atm, thermostat_time_constant=1.0000 ps, report_interval=100, restart_interval=100, core_alignment=True, com_distance_restraint=True, com_k=25 kcal mol-1 Å-2, com_restraint_width=5.0000 A, restraint=None, force_constant=10 kcal mol-1 Å-2, positional_restraint_width=0.5000 A, align_k_distance=2.5 kcal mol-1 Å-2, align_k_theta=10.0000 kcal/mol, align_k_psi=10.0000 kcal/mol, soft_core_umax=1000.0000 kcal/mol, soft_core_u0=500.0000 kcal/mol, soft_core_a=0.0625, use_atm_force=False, direction=1, lambda1=0.0, lambda2=0.0, alpha=0.0000e+00 kcal/mol, uh=0.0000e+00 kcal/mol, W0=0.0000e+00 kcal/mol)

Equilibration protocol for ATM simulations.

__init__(system=None, data=None, timestep=2.0000 fs, runtime=0.2000 ns, temperature_start=300.0000 K, temperature_end=300.0000 K, temperature=None, pressure=1.0000 atm, thermostat_time_constant=1.0000 ps, report_interval=100, restart_interval=100, core_alignment=True, com_distance_restraint=True, com_k=25 kcal mol-1 Å-2, com_restraint_width=5.0000 A, restraint=None, force_constant=10 kcal mol-1 Å-2, positional_restraint_width=0.5000 A, align_k_distance=2.5 kcal mol-1 Å-2, align_k_theta=10.0000 kcal/mol, align_k_psi=10.0000 kcal/mol, soft_core_umax=1000.0000 kcal/mol, soft_core_u0=500.0000 kcal/mol, soft_core_a=0.0625, use_atm_force=False, direction=1, lambda1=0.0, lambda2=0.0, alpha=0.0000e+00 kcal/mol, uh=0.0000e+00 kcal/mol, W0=0.0000e+00 kcal/mol)

Create a new equilibration protocol.

Parameters:

• system (System <BioSimSpace._SireWrappers.System>`) – A prepared ATM system.

• data (dict) – The ATM data dictionary.

• timestep (str, Time) – The integration timestep.

• runtime (str, Time) – The running time.

• temperature_start (str, Temperature) – The starting temperature.

• temperature_end (str, Temperature) – The ending temperature.

• temperature (str, Temperature) – The equilibration temperature. This takes precedence of over the other temperatures, i.e. to run at fixed temperature.

• pressure (str, Pressure) – The pressure. Pass pressure=None to use the NVT ensemble.

• thermostat_time_constant (str, Time) – Time constant for thermostat coupling.

• report_interval (int) – The frequency at which statistics are recorded. (In integration steps.)

• restart_interval (int) – The frequency at which restart configurations and trajectory

• core_alignment (bool) – Whether to use rigid core restraints to align the two ligands.

• align_k_distance (int, float, str, GeneralUnit) – The force constant for the distance portion of the alignment restraint (kcal/(mol A^2).

• align_k_theta (int, float, str, Energy) – The force constant for the angular portion of the alignment restaint (kcal/mol).

• align_k_psi (int, float, str, Energy) – The force constant for the dihedral portion of the alignment restraint (kcal/mol).

• com_distance_restraint (bool) – Whether to use a center of mass distance restraint. This restraint applies to the protein/host and both ligands, and is used to maintain the relative positions of all of them.

• com_k (int, float, str, GeneralUnit) – The force constant for the center of mass distance restraint (kcal/mol/A^2).

• com_restraint_width (int, float, str, :class:`Length <BioSimSpace.Types.Length>) – The width (tolerance) of the center of mass distance restraint (A).

• restraint (str, [int]) –

  The type of restraint to perform. This should be one of the following options:

  ”backbone”

  Protein backbone atoms. The matching is done by a name template, so is unreliable on conversion between molecular file formats.

  ”heavy”

  All non-hydrogen atoms that aren’t part of water molecules or free ions.

  ”all”

  All atoms that aren’t part of water molecules or free ions.

  Alternatively, the user can pass a list of atom indices for more fine-grained control. If None, then no restraints are used.

• force_constant (float, GeneralUnit) – The force constant for the restraint potential (kcal/(mol A^2).

• positional_restraint_width (float, Length) – The width of the flat-bottom potential used for coordinate restraint in Angstroms.

• pos_restrained_atoms ([int]) – The atoms to be restrained.

• soft_core_umax (int, float, str, Energy) – The Umax value for the ATM softcore potential (kcal/mol).

• soft_core_u0 (int, float, str, Energy) – The uh value for the ATM softcore potential (kcal/mol).

• soft_core_a (int, float, str, Energy) – The a value for the ATM softcore potential.

use_atm_forcebool

Whether to apply the ATM force within the equilibration protocol.

directionstr

The direction of the equilibration. Ignored if use_atm_force is False.

lambda1float

The lambda1 value for the ATM force. Ignored if use_atm_force is False.

lambda2float

The lambda2 value for the ATM force. Ignored if use_atm_force is False.

alphaint, float, str, Energy

The alpha value for the ATM force. Ignored if use_atm_force is False. Value in kcal/mol.

uhint, float, str, Energy

The uh value for the ATM force. Ignored if use_atm_force is False. Value in kcal/mol.

W0int, float, str, Energy

The W0 value for the ATM force. Ignored if use_atm_force is False. Value in kcal/mol.

Methods

__init__([system, data, timestep, runtime, ...])	Create a new equilibration protocol.
getAlignKDistance()	Return the align_k_distance value.
getAlignKPsi()	Return the align_k_psi value.
getAlignKTheta()	Return the align_k_theta value.
getAlpha()	Return the alpha value for the ATM force.
getCOMDistanceRestraint()	Return CMCM restraint boolean.
getCOMWidth()	Return the com_restraint_width value.
getCOMk()	Return the com_k value.
getCoreAlignment()	Return core alignment boolean.
getData()	Return the ATM data dictionary.
getDirection()	Return the direction of the equilibration.
getEndTemperature()	Return the final temperature.
getForceConstant()	Return the force constant for the restraint.
getLambda1()	Return the lambda1 value for the ATM force.
getLambda2()	Return the lambda2 value for the ATM force.
getPosRestWidth()	Return the width of the position restraint.
getPressure()	Return the pressure.
getReportInterval()	Return the interval between reporting statistics.
getRestartInterval()	Return the interval between saving restart confiugrations, and/or trajectory frames.
getRestraint()	Return the type of restraint.
getRunTime()	Return the running time.
getSoftCoreA()	Return the soft_core_a value.
getSoftCoreU0()	Return the soft_core_u0 value.
getSoftCoreUmax()	Return the soft_core_umax value.
getStartTemperature()	Return the starting temperature.
getThermostatTimeConstant()	Return the time constant for the thermostat.
getTimeStep()	Return the time step.
getUh()	Return the uh value for the ATM force.
getUseATMForce()	Return the use_atm_force flag.
getW0()	Return the W0 value for the ATM force.
isConstantTemp()	Return whether the protocol has a constant temperature.
restraints()	Return a list of the supported restraint keywords.
setAlignKDistance(align_k_distance)	Set the align_k_distance value.
setAlignKPsi(align_k_psi)	Set the align_k_psi value.
setAlignKTheta(align_k_theta)	Set the align_k_theta value.
setAlpha(alpha)	Set the alpha value for the ATM force.
setCOMDistanceRestraint(com_distance_restraint)	Set the CMCM restraint flag.
setCOMWidth(com_restraint_width)	Set the com_restraint_width value.
setCOMk(com_k)	Set the com_k value.
setCoreAlignment(core_alignment)	Set the core alignment flag.
setDirection(direction)	Set the direction of the equilibration.
setEndTemperature(temperature)	Set the final temperature.
setForceConstant(force_constant)	Set the force constant for the restraint.
setLambda1(lambda1)	Set the lambda1 value for the ATM force.
setLambda2(lambda2)	Set the lambda2 value for the ATM force.
setPosRestWidth(positional_restraint_width)	Set the width of the position restraint.
setPressure(pressure)	Set the pressure.
setReportInterval(report_interval)	Set the interval at which statistics are reported.
setRestartInterval(restart_interval)	Set the interval between saving restart confiugrations, and/or trajectory frames.
setRestraint(restraint)	Set the type of restraint.
setRuntime(runtime)	Set the running time.
setSoftCoreA(soft_core_a)	Set the soft_core_a value.
setSoftCoreU0(soft_core_u0)	Set the soft_core_u0 value.
setSoftCoreUmax(soft_core_umax)	Set the soft_core_umax value.
setStartTemperature(temperature)	Set the starting temperature.
setThermostatTimeConstant(...)	Set the time constant for the thermostat.
setTimestep(timestep)	Set the time step.
setUh(uh)	Set the uh value for the ATM force.
setUseATMForce(use_atm_force)	Set the use_atm_force flag.
setW0(W0)	Set the W0 value for the ATM force.

getAlignKDistance()

Return the align_k_distance value.

Returns:

align_k_distance – The align_k_distance value in kcal/mol angstrom**2.

Return type:

GeneralUnit

getAlignKPsi()

Return the align_k_psi value.

Returns:

align_k_psi – The align_k_psi value in kcal/mol.

Return type:

Energy

getAlignKTheta()

Return the align_k_theta value.

Returns:

align_k_theta – The align_k_theta value in kcal/mol.

Return type:

Energy

getAlpha()

Return the alpha value for the ATM force.

Returns:

alpha – The alpha value for the ATM force in kcal/mol. Ignored if use_atm_force is False.

Return type:

Energy

getCOMDistanceRestraint()

Return CMCM restraint boolean.

Returns:

com_distance_restraint – Whether to use the CMCM restraint.

Return type:

bool

getCOMWidth()

Return the com_restraint_width value.

Returns:

com_restraint_width – The com_restraint_width value in angstroms.

Return type:

Length

getCOMk()

Return the com_k value.

Returns:

com_k – The com_k value in kcal/mol A**2.

Return type:

GeneralUnit

getCoreAlignment()

Return core alignment boolean.

Returns:

core_alignment – Whether to use core alignment.

Return type:

bool

getData()

Return the ATM data dictionary.

Returns:

data – The ATM data dictionary.

Return type:

dict

getDirection()

Return the direction of the equilibration.

Returns:

direction – The direction of the equilibration. Ignored if use_atm_force is False.

Return type:

str

getEndTemperature()

Return the final temperature.

Returns:

temperature – The final temperature.

Return type:

Temperature

getForceConstant()

Return the force constant for the restraint.

Returns:

force_constant – The force constant for the restraint, in units of kcal_per_mol/angstrom**2.

Return type:

float, str, class:GeneralUnit

getLambda1()

Return the lambda1 value for the ATM force.

Returns:

lambda1 – The lambda1 value for the ATM force. Ignored if use_atm_force is False.

Return type:

float

getLambda2()

Return the lambda2 value for the ATM force.

Returns:

lambda2 – The lambda2 value for the ATM force. Ignored if use_atm_force is False.

Return type:

float

getPosRestWidth()

Return the width of the position restraint.

Returns:

positional_restraint_width – The width of the position restraint.

Return type:

Length

getPressure()

Return the pressure.

Returns:

pressure – The pressure.

Return type:

Pressure

getReportInterval()

Return the interval between reporting statistics. (In integration steps.). :returns: report_interval – The number of integration steps between reporting statistics. :rtype: int

getRestartInterval()

Return the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).

Returns:

restart_interval – The number of integration steps between saving restart configurations and/or trajectory frames.

Return type:

int

getRestraint()

Return the type of restraint.

Returns:

restraint – The type of restraint, either a keyword or a list of atom indices.

Return type:

str, [int]

getRunTime()

Return the running time.

Returns:

runtime – The simulation run time.

Return type:

Time

getSoftCoreA()

Return the soft_core_a value.

Returns:

soft_core_a – The soft_core_a value.

Return type:

float

getSoftCoreU0()

Return the soft_core_u0 value.

Returns:

soft_core_u0 – The soft_core_u0 value in kcal/mol.

Return type:

Energy

getSoftCoreUmax()

Return the soft_core_umax value.

Returns:

soft_core_umax – The soft_core_umax value in kcal/mol.

Return type:

Energy

getStartTemperature()

Return the starting temperature.

Returns:

temperature – The starting temperature.

Return type:

Temperature

getThermostatTimeConstant()

Return the time constant for the thermostat.

Returns:

runtime – The time constant for the thermostat.

Return type:

Time

getTimeStep()

Return the time step.

Returns:

time – The integration time step.

Return type:

Time

getUh()

Return the uh value for the ATM force.

Returns:

uh – The uh value for the ATM force in kcal/mol. Ignored if use_atm_force is False.

Return type:

Energy

getUseATMForce()

Return the use_atm_force flag.

Returns:

use_atm_force – Whether to apply the ATM force within the equilibration protocol.

Return type:

bool

getW0()

Return the W0 value for the ATM force.

Returns:

W0 – The W0 value for the ATM force in kcal/mol. Ignored if use_atm_force is False.

Return type:

Energy

isConstantTemp()

Return whether the protocol has a constant temperature.

Returns:

is_const_temp – Whether the temperature is fixed.

Return type:

bool

classmethod restraints()

Return a list of the supported restraint keywords.

Returns:

restraints – A list of the supported restraint keywords.

Return type:

[str]

setAlignKDistance(align_k_distance)

Set the align_k_distance value.

Parameters:

align_k_distance (int, float, str, GeneralUnit, float) – Length value for the alignment restraint kcal/mol angstrom**2.

setAlignKPsi(align_k_psi)

Set the align_k_psi value.

Parameters:

align_k_psi (int, float, str, Energy) – Force constant for the alignment dihedral constraint in kcal/mol.

setAlignKTheta(align_k_theta)

Set the align_k_theta value.

Parameters:

align_k_theta (int, float, str, Energy) – Force constant for the alignment angular constraint in kcal/mol.

setAlpha(alpha)

Set the alpha value for the ATM force.

Parameters:

alpha (int, float, str, Energy) – The alpha value for the ATM force in kcal/mol. Ignored if use_atm_force is False.

setCOMDistanceRestraint(com_distance_restraint)

Set the CMCM restraint flag.

Parameters:

com_distance_restraint (bool) – Whether to use the CMCM restraint.

setCOMWidth(com_restraint_width)

Set the com_restraint_width value.

Parameters:

com_restraint_width (int, float, str, :class:`Length <BioSimSpace.Types.Length>) – The com_restraint_width value in angstroms.

setCOMk(com_k)

Set the com_k value.

Parameters:

com_k (int, float, str, :class:`GeneralUnit <BioSimSpace.Types._GeneralUnit>) – The force constant for the CM-CM force in kcal/mol A**2.

setCoreAlignment(core_alignment)

Set the core alignment flag.

Parameters:

core_alignment (bool) – Whether to use core alignment.

setDirection(direction)

Set the direction of the equilibration.

Parameters:

direction (str) – The direction of the equilibration. Ignored if use_atm_force is False.

setEndTemperature(temperature)

Set the final temperature.

Parameters:

temperature (str, Temperature) – The final temperature.

setForceConstant(force_constant)

Set the force constant for the restraint.

Parameters:

force_constant (int, float, str, GeneralUnit, float) – The force constant for the restraint, in units of kcal_per_mol/angstrom**2.

setLambda1(lambda1)

Set the lambda1 value for the ATM force.

Parameters:

lambda1 (float) – The lambda1 value for the ATM force. Ignored if use_atm_force is False.

setLambda2(lambda2)

Set the lambda2 value for the ATM force.

Parameters:

lambda2 (float) – The lambda2 value for the ATM force. Ignored if use_atm_force is False.

setPosRestWidth(positional_restraint_width)

Set the width of the position restraint.

Parameters:

positional_restraint_width (int, float, str, Length) – The width of the position restraint.

setPressure(pressure)

Set the pressure.

Parameters:

pressure (str, Pressure) – The pressure.

setReportInterval(report_interval)

Set the interval at which statistics are reported. (In integration steps.).

Parameters:

report_interval (int) – The number of integration steps between reporting statistics.

setRestartInterval(restart_interval)

Set the interval between saving restart confiugrations, and/or trajectory frames. (In integration steps.).

Parameters:

restart_interval (int) – The number of integration steps between saving restart configurations and/or trajectory frames.

setRestraint(restraint)

Set the type of restraint.

Parameters:

restraint (str, [int]) –

The type of restraint to perform. This should be one of the following options:

”backbone”

Protein backbone atoms. The matching is done by a name template, so is unreliable on conversion between molecular file formats.

”heavy”

All non-hydrogen atoms that aren’t part of water molecules or free ions.

”all”

All atoms that aren’t part of water molecules or free ions.

Alternatively, the user can pass a list of atom indices for more fine-grained control.

setRuntime(runtime)

Set the running time.

Parameters:

runtime (str, Time) – The simulation run time.

setSoftCoreA(soft_core_a)

Set the soft_core_a value.

Parameters:

soft_core_a (float) – The softcore a value.

setSoftCoreU0(soft_core_u0)

Set the soft_core_u0 value.

Parameters:

soft_core_u0 (int, float, str, Energy) – The softcore u0 value in kcal/mol.

setSoftCoreUmax(soft_core_umax)

Set the soft_core_umax value.

Parameters:

soft_core_umax (int, float, str, Energy) – The softcore Umax value in kcal/mol.

setStartTemperature(temperature)

Set the starting temperature.

Parameters:

temperature (str, Temperature) – The starting temperature.

setThermostatTimeConstant(thermostat_time_constant)

Set the time constant for the thermostat.

Parameters:

thermostat_time_constant (str, Time) – The time constant for the thermostat.

setTimestep(timestep)

Set the time step.

Parameters:

time (str, Time) – The integration time step.

setUh(uh)

Set the uh value for the ATM force.

Parameters:

uh (int, float, str, Energy) – The uh value for the ATM force in kcal/mol. Ignored if use_atm_force is False.

setUseATMForce(use_atm_force)

Set the use_atm_force flag.

Parameters:

use_atm_force (bool) – Whether to apply the ATM force within the equilibration protocol.

setW0(W0)

Set the W0 value for the ATM force.

Parameters:

W0 (int, float, str, Energy) – The W0 value for the ATM force in kcal/mol. Ignored if use_atm_force is False.