BioSimSpace.Protocol.FreeEnergy#

class BioSimSpace.Protocol.FreeEnergy(lam=0.0, lam_vals=None, min_lam=0.0, max_lam=1.0, num_lam=11, timestep=2.0000 fs, runtime=4.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, report_interval=200000, restart_interval=20000, perturbation_type='full')[source]#

A class for storing free energy protocols.

__init__(lam=0.0, lam_vals=None, min_lam=0.0, max_lam=1.0, num_lam=11, timestep=2.0000 fs, runtime=4.0000 ns, temperature=300.0000 K, pressure=1.0000 atm, report_interval=200000, restart_interval=20000, perturbation_type='full')[source]#

Constructor.

Parameters:

lam (float) – The perturbation parameter: [0.0, 1.0]
lam_vals ([float]) – The list of lambda parameters.
min_lam (float) – The minimum lambda value.
max_lam (float) – The maximum lambda value.
num_lam (int) – The number of lambda values.
timestep (Time) – The integration timestep.
runtime (Time) – The running time.
temperature (Temperature) – The temperature.
pressure (Pressure) – The pressure. Pass pressure=None to use the NVT ensemble.
report_interval (int) – The frequency at which statistics are recorded. (In integration steps.)
restart_interval (int) – The frequency at which restart configurations and trajectory
perturbation_type (str) –

The type of perturbation to perform. Options are:
”full” : A full perturbation of all terms (default option). “discharge_soft” : Perturb all discharging soft atom charge terms (i.e. value->0.0). “vanish_soft” : Perturb all vanishing soft atom LJ terms (i.e. value->0.0). “flip” : Perturb all hard atom terms as well as bonds/angles. “grow_soft” : Perturb all growing soft atom LJ terms (i.e. 0.0->value). “charge_soft” : Perturb all charging soft atom LJ terms (i.e. 0.0->value).

Currently perturubation_type != “full” is only supported by BioSimSpace.Process.Somd.

Methods

`__init__`([lam, lam_vals, min_lam, max_lam, ...])	Constructor.
`getLambda`()	Get the value of the perturbation parameter.
`getLambdaIndex`()	Get the index of the lambda value within the lambda array.
`getLambdaValues`()	Get the list of lambda values.
`getPerturbationType`()	Get the perturbation type.
`getPressure`()	Return the pressure.
`getReportInterval`()	Return the interval between reporting statistics.
`getRestartInterval`()	Return the interval between saving restart confiugrations, and/or trajectory frames.
`getRunTime`()	Return the running time.
`getTemperature`()	Return temperature.
`getTimeStep`()	Return the time step.
`setLambdaValues`(lam[, lam_vals, min_lam, ...])	Set the list of lambda values.
`setPerturbationType`(perturbation_type)	Set the perturbation type.
`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.
`setRunTime`(runtime)	Set the running time.
`setTemperature`(temperature)	Set the temperature.
`setTimeStep`(timestep)	Set the time step.

getLambda()[source]#

Get the value of the perturbation parameter.

Returns:: lam – The value of the perturbation parameter.
Return type:: float

getLambdaIndex()[source]#

Get the index of the lambda value within the lambda array.

Returns:: index – The index of the lambda value in teh lambda array.
Return type:: int

getLambdaValues()[source]#

Get the list of lambda values.

Returns:: lam_vals – The list of lambda values.
Return type:: [float]

getPerturbationType()[source]#

Get the perturbation type.

Returns:: perturbation_type – The perturbation type.
Return type:: str

getPressure()[source]#

Return the pressure.

Returns:: pressure – The pressure.
Return type:: Pressure

getReportInterval()[source]#

Return the interval between reporting statistics. (In integration steps.).

Returns:: report_interval – The number of integration steps between reporting statistics.
Return type:: int

getRestartInterval()[source]#

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

getRunTime()[source]#

Return the running time.

Returns:: runtime – The simulation run time.
Return type:: Time

getTemperature()[source]#

Return temperature.

Returns:: temperature – The simulation temperature.
Return type:: Temperature

getTimeStep()[source]#

Return the time step.

Returns:: timestep – The integration time step.
Return type:: Time

setLambdaValues(lam, lam_vals=None, min_lam=None, max_lam=None, num_lam=None)[source]#

Set the list of lambda values.

Parameters:

lam (float) – The perturbation parameter: [0.0, 1.0]
lam_vals ([float]) – A list of lambda values.
min_lam (float) – The minimum lambda value.
max_lam (float) – The maximum lambda value.
num_lam (int) – The number of lambda values.

setPerturbationType(perturbation_type)[source]#

Set the perturbation type.

Parameters:

perturbation_type (str) –

The type of perturbation to perform. Options are:: ”full” : A full perturbation of all terms (default option). “discharge_soft” : Perturb all discharging soft atom charge terms (i.e. value->0.0). “vanish_soft” : Perturb all vanishing soft atom LJ terms (i.e. value->0.0). “flip” : Perturb all hard atom terms as well as bonds/angles. “grow_soft” : Perturb all growing soft atom LJ terms (i.e. 0.0->value). “charge_soft” : Perturb all charging soft atom LJ terms (i.e. 0.0->value).

setPressure(pressure)[source]#

Set the pressure.

Parameters:: pressure (Pressure) – The pressure.

setReportInterval(report_interval)[source]#

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)[source]#

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.

setRunTime(runtime)[source]#

Set the running time.

Parameters:: runtime (Time) – The simulation run time.

setTemperature(temperature)[source]#

Set the temperature.

Parameters:: temperature (Temperature) – The simulation temperature.

setTimeStep(timestep)[source]#

Set the time step.

Parameters:: timestep (Time) – The integration time step.