Introduction

The ACEMD3 input file may contain any of the commands listed below.

Each command must start on a new line and be followed by its arguments. Commands are case-insensitive, but their arguments may be case-sensitive.

Blank lines are permitted. Lines beginning with a “#” are treated as comments and ignored.

Forcefield Configuration

parmfile

  • Default: [none]

The filename of an Amber PRMTOP file

parameters

  • Default: [none]

The filename of a CHARMM PAR file. May be specified more than once.

Initial State

structure

  • Default: [none]

The filename of a CHARMM PSF file

coordinates

  • Default: structure.pdb

Mandatory initial system geometry in PDB format.

binCoordinates

  • Default: [none]

Optional initial system geometry in NAMD BINCOOR format. If specified, overrides “coordinates”

velocities

  • Default: [none]

Optional initial system velocity field in NAMD BINCOOR format. If specified, overrides field generated by “temperature”

binVelocities

  • Default: [none]

Optional initial system velocity field in NAMD BINCOOR format. If specified, overrides field generated by “temperature” and “velocities”

extendedSystem

  • Default: [none]

Filename of a NAMD XSC format file giving the periodic cell dimensions. Overrides “celldimension” and any dimensions in the “coordinates” PDB

temperature

  • Default: 0.

The temperature in Kelvin for which to generate an initial velocity field.

celldimension

  • 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.

Output

ACEMD3 will always output output.coor, output.vel and output.xsc at the end of a simulation. Additionally, it will periodically write out the coordinate state to an XTC format trajectory file. Note that DCD format is no longer supported.

trajectoryFile [output.xtc]

  • Default output.xtc

The name of the trajectory file to write to.

trajectoryFreq

  • Default 25000

The number of steps between outputting coordinates to the trajectory file

Electrostatics

PME

  • Default: on

Use particle-mesh Ewald summation for long-range electrostatics.

cutoff

  • Default: 9.

Real-space cutoff in Angstroms for electrostatics and van der Waals.

switching

  • Default: on

Apply switching function to the van der Waals potential.

switchDist

  • Default: 7.5

Distance in Angstrom at which to begin applying the switching function.

Temperature Control

ACEMD3 continues to use a Langevin thermostat. Old commands with the “langevin” prefix will be converted to their new equivalents and a warning issued.

thermostat

  • Default: off

Enable thermostatic control

thermostatTemp

  • Default: 300.

Target temperature (K) for thermostatic control

thermostatDamping

  • Default: 0.1

Damping constant for the Langevin thermostat in ps^-1

Pressure Control

The barostat algorithm in ACEMD3 has changed from Berendsen to a non-virial Monte Carlo scheme. Old commands with the “berendsen” prefix will be converted to their new equivalents and a warning issued.

barostat

  • Default: off

Enable pressure control.

barostatPressure

  • Default: 1.0

The target pressure in bar.

useFlexibleCell

  • Default: False

Allow X, Y and Z unit cell dimensions to vary independently

useConstantArea

  • Default: False

Constrain the X,Y dimensions of the unit cell. Allow Z to vary independently.

useConstantRatio

  • Default: False

Constrain the X:Y radio of the unit cell dimensions. Allow Z to vary independently.

Metadynamics

PlumedFile

  • Default: [none]

The filename of a PLUMED2 input file. If set, enables PLUMED metadynamics

Restraints

For more details on the use of these new commands please read Applying Restraints

atomRestraint

Specify a restraining potential centred on specific atom centres.

groupRestraint

Specify a restraining potential centred on a group of atoms.

Integration

timestep

  • Default: 4.

The integration timestep in femtoseconds. Note that if timestep >= 2.0 then constraints will be applied to all bonded terms including an H. Additionally, if timestep >= 4.0 hydrogen mass repartitioning is performed, increasing the mass of H to 4au.

Run Configuration

restart

  • Default: off

If set, attempt to restart a simulation from checkpoint files. Restart files are always written every trajectoryFreq steps irrespective of this setting.

minimize

  • Default: 0

The number of energy minimization steps to perform before commencing dynamics.

run

  • Default: 0

The length of simulation to run. May be specified as a number of steps or as a time if one of the suffices “us”, “ns”, “ps”, “fs” is used.