Skip to content

Molecular Dynamics Workflow

Purpose: Molecular-dynamics workflow with thermostat/barostat/shear settings and ensemble outputs

Relationship map

Hold "Alt" / "Option" to enable pan & zoom 
classDiagram
    class BarostatParameters
    class CorrelationFunction
    class DiffusionConstant
    class EnsembleProperty
    class FreeEnergyCalculationParameters
    class Lambdas
    class MDSettings
    class MeanSquaredDisplacement
    class MolecularDynamics
    class MolecularDynamicsMethod
    class MolecularDynamicsResults
    class NumericalSettings
    class PhysicalProperty
    class RadialDistributionFunction
    class SerialWorkflow
    class SerialWorkflowResults
    class ShearParameters
    class SimulationWorkflowMethod
    class ThermostatParameters
    MDSettings <|-- BarostatParameters
    PhysicalProperty <|-- CorrelationFunction
    EnsembleProperty <|-- DiffusionConstant
    PhysicalProperty <|-- EnsembleProperty
    MDSettings <|-- FreeEnergyCalculationParameters
    NumericalSettings <|-- MDSettings
    CorrelationFunction <|-- MeanSquaredDisplacement
    SerialWorkflow <|-- MolecularDynamics
    SimulationWorkflowMethod <|-- MolecularDynamicsMethod
    SerialWorkflowResults <|-- MolecularDynamicsResults
    EnsembleProperty <|-- RadialDistributionFunction
    MDSettings <|-- ShearParameters
    MDSettings <|-- ThermostatParameters
    FreeEnergyCalculationParameters *-- Lambdas : lambdas
    MolecularDynamics *-- MolecularDynamicsMethod : method
    MolecularDynamics *-- MolecularDynamicsResults : results
    MolecularDynamicsMethod *-- BarostatParameters : barostat_parameters
    MolecularDynamicsMethod *-- FreeEnergyCalculationParameters : free_energy_calculation_parameters
    MolecularDynamicsMethod *-- ShearParameters : shear_parameters
    MolecularDynamicsMethod *-- ThermostatParameters : thermostat_parameters
    MolecularDynamicsResults *-- DiffusionConstant : diffusion_constants
    MolecularDynamicsResults *-- MeanSquaredDisplacement : mean_squared_displacements
    MolecularDynamicsResults *-- RadialDistributionFunction : radial_distribution_functions

Legend

inheritance (is-a)
composition (has-a)

Quantities by Key Sections

SerialWorkflow

Section Description MetaInfo
SerialWorkflow Base class for workflows where tasks are executed sequentially. Open in MetaInfo browser

This section has no direct quantities.

SerialWorkflowResults

Section Description MetaInfo
SerialWorkflowResults Open in MetaInfo browser

This section has no direct quantities.

SimulationWorkflowMethod

Section Description MetaInfo
SimulationWorkflowMethod Open in MetaInfo browser

This section has no direct quantities.

NumericalSettings

Section Description MetaInfo
NumericalSettings A base section used to define how a chosen ModelMethod is realized numerically in a simulation. Open in MetaInfo browser
Quantity Type Description
name m_str(str) Name of the numerical settings section. This is typically used for easy identification of the NumericalSettings section within a ModelMethod. Possible values: "KMesh", "FrequencyMesh", "TimeMesh", "SelfConsistency", "BasisSet".

PhysicalProperty

Section Description MetaInfo
PhysicalProperty A base section for computational output properties, containing all relevant (meta)data. Open in MetaInfo browser
Quantity Type Description
name m_str(str) Name of the physical property. Example: 'ElectronicBandGap'.
iri URL Internationalized Resource Identifier (IRI) pointing to a definition, typically within a larger, ontological framework.
type m_str(str) Type categorization of the physical property. Example: an ElectronicBandGap can be 'direct' or 'indirect'.
contribution_type m_str(str) Type of contribution to the physical property. Hence, only applies to contributions instances. Example: TotalEnergy may have contributions like kinetic, potential, etc.
label m_str(str) Label for additional classification of the physical property. Example: an ElectronicBandGap can be labeled as 'DFT' or 'GW' depending on the methodology used to calculate it.
entity_ref Reference
Reference to the entity that the physical property refers to.Reference to the entity that the physical property refers to. Examples:
- a simulated physical property might refer to the macroscopic system or instead of a specific atom in the unit
cell. In the first case, outputs.model_system_ref (see outputs.py) will point to the ModelSystem section,
while in the second case, entity_ref will point to AtomsState section (see atoms_state.py).
is_derived m_bool(bool)
Flag indicating whether the physical property is derived from other physical properties.Flag indicating whether the physical property is derived from other physical properties. We make
the distinction between directly parsed and derived physical properties:
- Directly parsed: the physical property is directly parsed from the simulation output files.
- Derived: the physical property is derived from other physical properties. No extra numerical settings
are required to calculate the physical property.
physical_property_ref Reference Reference to the PhysicalProperty section from which the physical property was derived. If physical_property_ref is populated, the quantity is_derived is set to True via normalization.
is_converged m_bool(bool) Flag indicating whether the calculation that yields this physical property is converged or not after a SCF or optimization process. This information is obtained from the workflow section.

MDSettings

Section Description MetaInfo
MDSettings Abstract class for classifying numerical settings relevant for molecular dynamics runs. Open in MetaInfo browser
Quantity Type Description
frame_start m_int32(int) Trajectory frame number where the application of these settings start.
frame_end m_int32(int) Trajectory frame number where the application of these settings end.

ThermostatParameters

Section Description MetaInfo
ThermostatParameters Section containing the parameters pertaining to the thermostat for a molecular dynamics run. Open in MetaInfo browser
Quantity Type Description
thermostat_type Enum
The name of the thermostat used for temperature control.The name of the thermostat used for temperature control. If skipped or an empty string is used, it
means no thermostat was applied.
Allowed values are:
| Thermostat Name | Description |
| ---------------------- | ----------------------------------------- |
| "" | No thermostat |
| "andersen" | H.C. Andersen, J. Chem. Phys.
72, 2384 (1980) |
| "berendsen" | H. J. C. Berendsen, J. P. M. Postma,
W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys.
81, 3684 (1984) |
| "brownian" | Brownian Dynamics |
| "dissipative_particle_dynamics" | R.D. Groot and P.B. Warren
J. Chem. Phys. 107(11), 4423-4435 (1997) |
| "langevin_goga" | N. Goga, A. J. Rzepiela, A. H. de Vries,
S. J. Marrink, and H. J. C. Berendsen, [J. Chem. Theory Comput. 8, 3637 (2012)]
(https://doi.org/10.1021/ct3000876) |
| "langevin_leap_frog" | J.A. Izaguirre, C.R. Sweet, and V.S. Pande
Pac Symp Biocomput. 15, 240-251 (2010) |
| "langevin_schneider" | T. Schneider and E. Stoll,
Phys. Rev. B 17, 1302 |
| "nose_hoover" | S. Nosé, [Mol. Phys. 52, 255 (1984)]
(https://doi.org/10.1080/00268978400101201); W.G. Hoover, [Phys. Rev. A
31, 1695 (1985) |
| "velocity_rescaling" | G. Bussi, D. Donadio, and M. Parrinello,
J. Chem. Phys. 126, 014101 (2007) |
| "velocity_rescaling_langevin" | G. Bussi and M. Parrinello,
Phys. Rev. E 75, 056707 (2007) |
| "velocity_rescaling_woodcock" | L. V. Woodcock,
Chem. Phys. Lett. 10, 257 (1971) |
reference_temperature m_float64(float64) The target temperature for the simulation. Typically used when temperature_profile is "constant".
coupling_constant m_float64(float64) The time constant for temperature coupling. Need to describe what this means for the various thermostat options...
effective_mass m_float64(float64) The effective or fictitious mass of the temperature resevoir.
temperature_profile Enum Type of temperature control (i.e., annealing) procedure. Can be "constant" (no annealing), "linear", or "exponential". If linear, "temperature_update_delta" specifies the corresponding update parameter. If exponential, "temperature_update_factor" specifies the corresponding update parameter.
reference_temperature_start m_float64(float64) The initial target temperature for the simulation. Typically used when temperature_profile is "linear" or "exponential".
reference_temperature_end m_float64(float64) The final target temperature for the simulation. Typically used when temperature_profile is "linear" or "exponential".
temperature_update_frequency m_int32(int) Number of simulation steps between changing the target temperature.
temperature_update_delta m_float64(float64) Amount to be added (subtracted if negative) to the current reference_temperature at a frequency of temperature_update_frequency when temperature_profile is "linear". The reference temperature is then replaced by this new value until the next update.
temperature_update_factor m_float64(float64) Factor to be multiplied to the current reference_temperature at a frequency of temperature_update_frequency when temperature_profile is exponential. The reference temperature is then replaced by this new value until the next update.
step_start m_int32(int) Trajectory step where this thermostating starts.
step_end m_int32(int) Trajectory step number where this thermostating ends.

BarostatParameters

Section Description MetaInfo
BarostatParameters Section containing the parameters pertaining to the barostat for a molecular dynamics run. Open in MetaInfo browser
Quantity Type Description
barostat_type Enum
The name of the barostat used for temperature control.The name of the barostat used for temperature control. If skipped or an empty string is used, it
means no barostat was applied.
Allowed values are:
| Barostat Name | Description |
| ---------------------- | ----------------------------------------- |
| "" | No thermostat |
| "berendsen" | H. J. C. Berendsen, J. P. M. Postma,
W. F. van Gunsteren, A. DiNola, and J. R. Haak, J. Chem. Phys.
81, 3684 (1984) |
| "martyna_tuckerman_tobias_klein" | G.J. Martyna, M.E. Tuckerman, D.J. Tobias, and M.L. Klein,
Mol. Phys. 87, 1117 (1996);
M.E. Tuckerman, J. Alejandre, R. López-Rendón, A.L. Jochim, and G.J. Martyna,
J. Phys. A. 59, 5629 (2006)|
| "nose_hoover" | S. Nosé, [Mol. Phys. 52, 255 (1984)]
(https://doi.org/10.1080/00268978400101201); W.G. Hoover, [Phys. Rev. A
31, 1695 (1985) |
| "parrinello_rahman" | M. Parrinello and A. Rahman,
J. Appl. Phys. 52, 7182 (1981);
S. Nosé and M.L. Klein, [Mol. Phys. 50, 1055 (1983) |
| "stochastic_cell_rescaling" | M. Bernetti and G. Bussi,
J. Chem. Phys. 153, 114107 (2020) |
coupling_type Enum
Describes the symmetry of pressure coupling.Describes the symmetry of pressure coupling. Specifics can be inferred from the coupling constant
| Type | Description |
| ---------------------- | ----------------------------------------- |
| isotropic | Identical coupling in all directions. |
| semi_isotropic | Identical coupling in 2 directions. |
| anisotropic | General case. |
reference_pressure m_float64(float64) (shape: [3, 3]) The target pressure for the simulation, stored in a 3x3 matrix, indicating the values for individual directions along the diagonal, and coupling between directions on the off-diagonal. Typically used when pressure_profile is "constant".
coupling_constant m_float64(float64) (shape: [3, 3]) The time constants for pressure coupling, stored in a 3x3 matrix, indicating the values for individual directions along the diagonal, and coupling between directions on the off-diagonal. 0 values along the off-diagonal indicate no-coupling between these directions.
compressibility m_float64(float64) (shape: [3, 3])
An estimate of the system's compressibility, used for box rescaling, stored in a...An estimate of the system's compressibility, used for box rescaling, stored in a 3x3 matrix indicating the values for individual directions
along the diagonal, and coupling between directions on the off-diagonal. If None, it may indicate that these values
are incorporated into the coupling_constant, or simply that the software used uses a fixed value that is not available in
the input/output files.
pressure_profile Enum Type of pressure control procedure. Can be "constant" (no annealing), "linear", or "exponential". If linear, "pressure_update_delta" specifies the corresponding update parameter. If exponential, "pressure_update_factor" specifies the corresponding update parameter.
reference_pressure_start m_float64(float64) (shape: [3, 3]) The initial target pressure for the simulation, stored in a 3x3 matrix, indicating the values for individual directions along the diagonal, and coupling between directions on the off-diagonal. Typically used when pressure_profile is "linear" or "exponential".
reference_pressure_end m_float64(float64) (shape: [3, 3]) The final target pressure for the simulation, stored in a 3x3 matrix, indicating the values for individual directions along the diagonal, and coupling between directions on the off-diagonal. Typically used when pressure_profile is "linear" or "exponential".
pressure_update_frequency m_int32(int) Number of simulation steps between changing the target pressure.
pressure_update_delta m_float64(float64) Amount to be added (subtracted if negative) to the current reference_pressure at a frequency of pressure_update_frequency when pressure_profile is "linear". The pressure temperature is then replaced by this new value until the next update.
pressure_update_factor m_float64(float64) Factor to be multiplied to the current reference_pressure at a frequency of pressure_update_frequency when pressure_profile is exponential. The reference pressure is then replaced by this new value until the next update.
step_start m_int32(int) Trajectory step where this barostating starts.
step_end m_int32(int) Trajectory step number where this barostating ends.

ShearParameters

Section Description MetaInfo
ShearParameters Section containing the parameters pertaining to the shear flow for a molecular dynamics run. Open in MetaInfo browser
Quantity Type Description
shear_type Enum
The name of the method used to implement the effect of shear flow within the simulation.The name of the method used to implement the effect of shear flow within the simulation.
Allowed values are:
| Shear Method | Description |
| ---------------------- | ----------------------------------------- |
| "" | No thermostat |
| "lees_edwards" | A.W. Lees and S.F. Edwards,
J. Phys. C 5 (1972) 1921|
| "trozzi_ciccotti" | A.W. Lees and S.F. Edwards,
Phys. Rev. A 29 (1984) 916|
| "ashurst_hoover" | W. T. Ashurst and W. G. Hoover,
Phys. Rev. A 11 (1975) 658|
shear_rate m_float64(float64) (shape: [3, 3])
The external stress tensor include normal (diagonal elements; which are zero in ...The external stress tensor include normal (diagonal elements; which are zero in shear simulations)
and shear stress' rates (off-diagonal elements).
Its elements are: [[σ_x, τ_yx, τ_zx], [τ_xy, σ_y, τ_zy], [τ_xz, τ_yz, σ_z]],
where σ and τ are the normal and shear stress' rates.
The first and second letters in the index correspond to the normal vector to the shear plane and the direction of shearing, respectively.
step_start m_int32(int) Trajectory step where this shearing starts.
step_end m_int32(int) Trajectory step number where this shearing ends.

FreeEnergyCalculationParameters

Section Description MetaInfo
FreeEnergyCalculationParameters Parameters for a free energy workflow run. Open in MetaInfo browser
Quantity Type Description
calc_type Enum
Specifies the type of workflow.Specifies the type of workflow. Allowed values are:
| kind | Description |
| ---------------------- | ----------------------------------------- |
| "alchemical" | A non-physical transformation between 2 well-defined systems,
typically achieved by smoothly interpolating between Hamiltonians or force fields. |
| "umbrella_sampling" | A sampling of the path between 2 well-defined (sub)states of a system,
typically achieved by applying a biasing force to the force field along a
specified reaction coordinate.
current_lambda_index m_int32(int) Index into each Lambdas.lambda_values for the current simulation step/state (only valid if all targets share an aligned λ grid).
current_lambdas m_float64(float64) (shape: ['*']) Scalar λ per Lambdas entry order.
n_frames m_int32(int32) Number of time frames in the XVG free-energy output.
n_states m_int32(int32) Number of lambda states in the XVG free-energy differences.
times m_float64(float64) (shape: ['n_frames']) Simulation time for each frame in the XVG output.
energy_derivative m_float64(float64) (shape: ['n_frames']) dH/dλ at the current lambda state for each time frame, as written by GROMACS to the XVG file.
energy_differences m_float64(float64) (shape: ['n_frames', 'n_states']) ΔH between the current lambda state and each other state for each time frame (n_states columns in the XVG file).
pv_energy m_float64(float64) (shape: ['n_frames']) PV contribution to the free energy for each time frame.

Lambdas

Section Description MetaInfo
Lambdas Parameters for one lambda dimension / interaction type. Open in MetaInfo browser
Quantity Type Description
interaction_type Enum
The type of lambda interpolationThe type of lambda interpolation
Allowed values are:
| type | Description |
| ---------------------- | ----------------------------------------- |
| "output" | Lambdas for the free energy outputs saved.
These will also act as a default in case some
relevant lambdas are not specified. |
| "coulomb" | Lambdas for interpolating electrostatic interactions. |
| "vdw" | Lambdas for interpolating van der Waals interactions. |
| "bonded" | Lambdas for interpolating all intramolecular interactions. |
| "restraint" | Lambdas for interpolating restraints. |
| "mass" | Lambdas for interpolating masses. |
| "temperature" | Lambdas for interpolating temperature. |
lambda_values m_float64(float64) (shape: ['*']) Grid of λ values for this interaction (e.g., [0.0, 0.1, …, 1.0]).
endpoints_on m_bool(bool) (shape: [2]) Specifies whether the interaction is ‘on’ at the endpoints: [initial@λ=0, final@λ=1].
scheme Enum Alchemical scheme for this interaction, if applicable.
softcore_enabled m_bool(bool) Soft-core on/off for nonbonded.
softcore_alpha m_float64(float64) Soft-core α parameter.
softcore_p m_int32(int32) Soft-core power p.
softcore_sigma m_float64(float64) Soft-core σ (if used).

EnsembleProperty

Section Description MetaInfo
EnsembleProperty Abstract base section for static observables calculated from a trajectory (i.e., from an ensemble average). Open in MetaInfo browser
Quantity Type Description
n_smooth m_int32(int) Number of bins over which the running average was computed for the observable `values'.
n_prune m_int32(int) Frequency with which to select frames for calculation of the observable `values'.
n_variables m_int32(int) Number of variables along which the property is determined.
variables_name m_str(str) (shape: ['n_variables']) Name/description of the independent variables along which the observable is defined.
n_bins m_int32(int) Number of bins.
frame_start m_int32(int) Trajectory frame number where the ensemble averaging starts.
frame_end m_int32(int) Trajectory frame number where the ensemble averaging ends.

CorrelationFunction

Section Description MetaInfo
CorrelationFunction Abstract base section for time correlation functions calculated from a trajectory. Open in MetaInfo browser
Quantity Type Description
direction Enum Describes the direction in which the correlation function was calculated.
n_times m_int32(int) Number of times windows for the calculation of the correlation function.
times m_float64(float64) (shape: ['n_times']) Time windows used for the calculation of the correlation function.

RadialDistributionFunction

Section Description MetaInfo
RadialDistributionFunction Section containing information about the calculation of radial distribution functions (rdfs). Open in MetaInfo browser
Quantity Type Description
bins m_float64(float64) (shape: ['n_bins']) Distances along which the rdf was calculated.
value m_float64(float64) (shape: ['n_bins']) Values of the property.

DiffusionConstant

Section Description MetaInfo
DiffusionConstant Section containing information regarding the diffusion constants. Open in MetaInfo browser
Quantity Type Description
value m_float64(float64) Values of the diffusion constants.

MeanSquaredDisplacement

Section Description MetaInfo
MeanSquaredDisplacement Section containing information about a calculation of any mean squared displacements (msds). Open in MetaInfo browser
Quantity Type Description
value m_float64(float64) (shape: ['n_times']) Mean squared displacement values.

MolecularDynamics

Section Description MetaInfo
MolecularDynamics Open in MetaInfo browser

This section has no direct quantities.

MolecularDynamicsMethod

Section Description MetaInfo
MolecularDynamicsMethod Open in MetaInfo browser
Quantity Type Description
thermodynamic_ensemble Enum
The type of thermodynamic ensemble that was simulated.The type of thermodynamic ensemble that was simulated.
Allowed values are:
| Thermodynamic Ensemble | Description |
| ---------------------- | ----------------------------------------- |
| "NVE" | Constant number of particles, volume, and energy |
| "NVT" | Constant number of particles, volume, and temperature |
| "NPT" | Constant number of particles, pressure, and temperature |
| "NPH" | Constant number of particles, pressure, and enthalpy |
integrator_type Enum
Name of the integrator.Name of the integrator.
Allowed values are:
| Integrator Name | Description |
| ---------------------- | ----------------------------------------- |
| "langevin_goga" | N. Goga, A. J. Rzepiela, A. H. de Vries,
S. J. Marrink, and H. J. C. Berendsen, [J. Chem. Theory Comput. 8, 3637 (2012)]
(https://doi.org/10.1021/ct3000876) |
| "langevin_schneider" | T. Schneider and E. Stoll,
Phys. Rev. B 17, 1302 |
| "leap_frog" | R.W. Hockney, S.P. Goel, and J. Eastwood,
J. Comp. Phys. 14, 148 (1974) |
| "velocity_verlet" | W.C. Swope, H.C. Andersen, P.H. Berens, and K.R. Wilson,
J. Chem. Phys. 76, 637 (1982) |
| "rRESPA_multitimescale" | M. Tuckerman, B. J. Berne, and G. J. Martyna
J. Chem. Phys. 97, 1990 (1992) |
| "langevin_leap_frog" | J.A. Izaguirre, C.R. Sweet, and V.S. Pande
Pac Symp Biocomput. 15, 240-251 (2010) |
integration_timestep m_float64(float64) The timestep at which the numerical integration is performed.
n_steps m_int32(int) Number of timesteps performed.
coordinate_save_frequency m_int32(int) The number of timesteps between saving the coordinates.
velocity_save_frequency m_int32(int) The number of timesteps between saving the velocities.
force_save_frequency m_int32(int) The number of timesteps between saving the forces.
thermodynamics_save_frequency m_int32(int) The number of timesteps between saving the thermodynamic quantities.

MolecularDynamicsResults

Section Description MetaInfo
MolecularDynamicsResults Open in MetaInfo browser
Quantity Type Description
n_steps m_int32(int32) Number of trajectory steps
trajectory Reference (shape: ['n_steps']) Reference to the system of each step in the trajectory.