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acemd.protocols module#

acemd.protocols.setup_equilibration(builddir: Path, outdir: Path, run: str | int, temperature: float = 300, extforces: dict | None = None, coordinates: Path | None = None, structure: Path | None = None, parameters: Path | None = None, barostatconstratio: bool = False, defaultrestraints: bool = True, restraintdecay: str | int | None = None, cispeptidebondcheck: bool = True, **kwargs)#

Set up an ACEMD equilibration simulation.

Parameters:

  • builddir (Path) – The directory containing the input files. Usually the output of a builder

  • outdir (Path) – The directory to write the input files and simulation output to

  • run (int or str) – The number of steps to run the simulation for

  • temperature (float, optional) – The temperature to equilibrate the system to, by default 300

  • extforces (dict, optional) – External forces to apply to the system

  • coordinates (Path, optional) – The coordinates file to use for the simulation. If None it will be auto-detected.

  • structure (Path, optional) – The structure file to use for the simulation. If None it will be auto-detected.

  • parameters (Path, optional) – The parameters file to use for the simulation. If None it will be auto-detected.

  • barostatconstratio (bool, optional) – Whether to use the barostatconstratio option. This is required for membrane simulations where the box should scale isotropically in the xy plane.

  • defaultrestraints (bool, optional) – Whether to use the default restraints. This will apply positional restraints to all protein CA atoms with 1 kcal/mol/A^2, all non-hydrogen protein atoms with 0.1 kcal/mol/A^2, all nucleic acid backbone atoms with 1 kcal/mol/A^2 and all nucleic acid atoms that are not part of the backbone with 0.1 kcal/mol/A^2.

  • restraintdecay (int or str, optional) – The restraint decay time. If set to a timestep or time, the restraints will scale to their initial value to 0 over the given restraintdecay time. Otherwise the restraints will scale to 0 over half the simulation time.

  • cispeptidebondcheck (bool, optional) – Whether to check for cis peptide bonds in the system. This will print a warning if any are found.

Notes

The function accepts additional keyword arguments to pass to the ACEMD input file. Please refer to the ACEMD documentation. All input file options can be used here.

Examples

>>> from acemd.protocols import setup_equilibration
>>> setup_equilibration(builddir, outdir, run="10ns")
>>> setup_equilibration(builddir, outdir, run="10ns", minimize=1000)
In the second example we override the default minimization steps of the protocol.
You can override any of the input file options of ACEMD.
acemd.protocols.setup_production(equildir: Path, outdir: Path, run: str | int, temperature: float = 300, extforces: dict | None = None, coordinates: Path | None = None, structure: Path | None = None, parameters: Path | None = None, cispeptidebondcheck: bool = True, **kwargs)#

Set up an ACEMD production simulation.

Parameters:

  • equildir (Path) – The directory containing the equilibrated system

  • outdir (Path) – The directory to write the input files and simulation output to

  • run (int or str) – The number of steps to run the simulation for

  • temperature (float, optional) – The temperature to run the simulation at, by default 300

  • extforces (dict, optional) – External forces to apply to the system

  • coordinates (Path, optional) – The coordinates file to use for the simulation. If None it will be auto-detected.

  • structure (Path, optional) – The structure file to use for the simulation. If None it will be auto-detected.

  • parameters (Path, optional) – The parameters file to use for the simulation. If None it will be auto-detected.

  • cispeptidebondcheck (bool, optional) – Whether to check for cis peptide bonds in the system. This will print a warning if any are found.

Notes

The function accepts additional keyword arguments to pass to the ACEMD input file. Please refer to the ACEMD documentation. All input file options can be used here.

Examples

>>> from acemd.protocols import setup_production
>>> setup_production(equildir, outdir, run="10ns")
This will autodetect the final coordinates and box size from the equilibrated system
and copy them over to set up a production simulation of 10 ns.
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