htmd.mdengine.acemd.acemd module

class htmd.mdengine.acemd.acemd.Acemd(config=None)

Bases: htmd.mdengine.acemd.acemd._Acemd

Class for configuring an ACEMD run.

Note: default=None means the parameter is not set, which means that ACEMD will use it’s own internal default. Check ACEMD documentation for its own defaults.

Parameters
  • temperature (float, default=None) – Temperature of the thermostat in Kelvin.

  • restart (str, default=None) – Restart simulation.

  • trajectoryfile (str, default=None) – Output file name.

  • trajectoryperiod (int, default=None) – Trajectory sampling frequency in steps.

  • timestep (int, default=None) – Simulation timestep.

  • pme (str, default=None) – Particle-mesh Ewald summation.

  • switching (str, default=None) – Apply switching function to the van der Waals potential.

  • switchdistance (float, default=None) – Distance in Angstrom at which to begin applying the switching function.

  • cutoff (float, default=None) – Real-space cutoff in Angstroms for electrostatics and van der Waals.

  • thermostat (str, default=None) – Enable thermostatic control

  • thermostattemperature (float, default=None) – Target temperature (K) for thermostatic control

  • thermostatdamping (float, default=None) – Damping constant for the Langevin thermostat in ps^-1

  • restraints (str, default=None) – Restraining potentials

  • barostat (str, default=None) – Enable pressure control

  • barostatpressure (float, default=None) – The target pressure in bar

  • barostatanisotropic (str, default=None) – Allow X, Y and Z unit cell dimensions to vary independently

  • barostatconstxy (str, default=None) – Constrain the X,Y dimensions of the unit cell. Allow Z to vary independently.

  • barostatconstratio (str, default=None) – Constrain the X:Y ratio of the unit cell dimensions. Allow Z to vary independently.

  • minimize (int, default=None) – The number of energy minimization steps to perform before commencing dynamics.

  • run (str, default=None) – The length of simulation ro run. May be specified as a number of steps or as a time if one of the suffices “us”, “ns”, “ps”, “fs” is used.

  • boxsize (str, default=None) – The dimensions of the unit cell in Angstrom. Note that the unit cell must be cuboid. Overrides any dimension given in the “coordinates” PDB.

  • implicit (str, default=None) – Set to True to enable implicit solvent simulations in AMBER.

  • Files

  • -----

  • these parameters to override the default search paths for these files. (Use) –

  • bincoordinates (str, default=None) – Optional initial system geometry in NAMD BINCOOR format. If specified, overrides “coordinates”

  • binvelocities (str, default=None) – Optional initial system velocity field in NAMD BINCOOR format. If specified, overrides field generated by “temperature” and “velocities”

  • structure (str, default=None) – The filename of a CHARMM PSF file

  • parameters (str, default=None) – The filename of a CHARMM PAR file

  • parmfile (str, default=None) – The filename of an Amber PRMTOP file

  • extendedsystem (str, default=None) – Filename of a NAMD XSC format file giving the periodic cell dimensions. Overrides “boxsize” and any dimensions in the “coordinates” PDB

  • coordinates (str, default=None) – Mandatory initial system geometry in PDB format

  • velocities (str, default=None) – Optional initial system velocity field in NAMD BINCOOR format. If specified, overrides field generated by “temperature”

Examples

>>> acemd = Acemd()
Or you can load preset configurations for ACEMD which search for default files and use recommended settings.
For example, to load the configuration for an equilibration run
>>> equil = Acemd('equilibration')  # Loads the Acemd configuration for equilibration runs
Now we write out the files needed for a run giving as input a folder containing the built structure files
>>> equil.write('./build/', './equil/')
Or to load the confifuration for a production run
>>> prod = Acemd('production')
>>> prod.write('./equil/', './prod/')
readConfig(configfile)
write(inputdir='.', outputdir='run', overwrite=False)
class htmd.mdengine.acemd.acemd.AtomRestraint(selection, width, restraints, axes='xyz')

Bases: htmd.mdengine.acemd.acemd._Restraint

class htmd.mdengine.acemd.acemd.GroupRestraint(selection, width, restraints, fbcentre=None, fbcentresel=None, axes='xyz')

Bases: htmd.mdengine.acemd.acemd._Restraint