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.

  • trajectoryfreq (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.

  • switchdist (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

  • thermostattemp (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

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

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

  • useconstantratio (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.

  • celldimension (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 “celldimension” 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.Acemd2

Bases: htmd.mdengine.acemd.acemd._Acemd

Class for legacy support of ACEMD older versions (“version 2”).

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

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

  • restartfreq (int, default=None) – Restart file frequency.

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

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

  • xtcfreq (int, default=None) – XTC sampling frequency in steps.

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

  • rigidbonds (('none', 'all'), str, default=None) – Enable holonomic constraints on all hydrogen-heavy atom bond terms

  • hydrogenscale (float, default=None) – Amount by which to scale the mass of H atoms

  • switching (('on', 'off'), str, default=None) – Enable to apply smoothing and switching functions to electrostatic and VdW forces.

  • switchdist (float, default=None) – Range beyond which to begin to apply the switching functions.

  • cutoff (str, default=None) – Cutoff distance for direct-space electrostatic interaction evaluation.

  • exclude (('none', '1-2', '1-3', '1-4', 'scaled1-4'), str, default=None) – Which pairs of bonded atoms should be excluded from non-bonded interactions

  • scaling14 (float, default=None) – Scaling factor for 1-4 electrostatic interations.

  • langevin (('on', 'off'), str, default=None) – Enable the Langevin thermostat.

  • langevintemp (float, default=None) – The set point in K for the Langevin thermostat.

  • langevindamping (float, default=None) – Langevin damping constant gamma (1/ps)

  • pme (('on', 'off'), str, default=None) – Enable the use of PME for long-range electrostatics.

  • pmegridspacing (float, default=None) – The spacing of the PME mesh in 1/A.

  • fullelectfrequency (int, default=None) – The frequency in interations between successive calculations of long-range (PME) electrostatics.

  • energyfreq (int, default=None) – The frequency with which ACEMD will calculate system energies.

  • constraints (('on', 'off'), str, default=None) – Set to enable positional constraints on specified atoms.

  • consref (str, default=None) – Specify a PDB file giving reference positions for constrained atoms.

  • constraintscaling (float, default=None) – The harmonic constraint energy function is multiplied by this parameter.

  • berendsenpressure (('on', 'off'), str, default=None) – Set to enable the Berendsen pressure bath barostatic control.

  • berendsenpressuretarget (float, default=None) – The target pressure (Bar) for the barostat.

  • berendsenpressurerelaxationtime (float, default=None) – Relaxation time for the barostat (fs).

  • tclforces (('on', 'off'), str, default=None) – Enable TCL force scripting.

  • minimize (int, default=None) – Number of steps of conjugate-gradient minimisation to perform.

  • run (str, default=None) – The number of simulation iterations to perform.

  • celldimension (str, default=None) – Dimensions of the unit cell.

  • useconstantratio (('on', 'off'), str, default=None) – Keep the ratio of the X-Y dimensions constant while allowing Z to fluctuate independently.

  • amber (('on', 'off'), str, default=None) – Indicate that the Amber force field is to be used.

  • dielectric (float, default=None) – Dielectric constant.

  • pairlistdist (str, default=None) – Specify the buffer size for grid cells.

  • TCL (str, default=None) – Extra TCL code to be prepended to the input file

  • Files

  • -----

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

  • bincoordinates (str, default=None) – Filename for initial structure coordinates, in NAMD Bincoor format.

  • binvelocities (str, default=None) – Initial velocity field, in NAMD Bincoor format.

  • binindex (str, default=None) – Filename for index file to set initial timestep (as made by a check-point)

  • structure (str, default=None) – CHARMM structure topology in PSF format

  • parameters (str, default=None) – CHARMM force-field parameter file (PRM)

  • extendedsystem (str, default=None) – If set, specifies an extended system .xsc file, from which a cell dimension will be read.

  • coordinates (str, default=None) – Filename for initial structure coordinates, in PDB format.

  • velocities (str, default=None) – Initial velocity field, in PDB format.

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

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