Reference

Command line arguments

Syntax:

acemd3 [--platform <platform>]
       [--ncups <n> | --ngpus <n> | --device <d1>[,<d2>,...]]
       [--help]
       <input>
--platform
  • Valid values: CPU, CUDA, OpenCL
  • Default: CUDA

Platform to use for a simulation. CUDA is for the GPUs from NVIDIA, while OpenCL is for the rest GPUs.

--ncpus
  • Valid values: positive integer
  • Default: all available CPUs

Number of CPUs to use for a simulation. This is only relevant for --platform CPU.

--ngpus
  • Valid values: positive integer
  • Default: 1

Number of GPUs to use for a simulation. This is only relevant for --platform CUDA or --platform OpenCL.

--device
  • Valid values: list of GPU indices
  • Default: none

List of GPU device indices to use for a simulation. The indices are separated by comma, but without spaces. If --device is set, it overrides --ngpus.

Run nvidia-smi to get the available device indices.

Example:

acemd3 --device 0,2
--help
  • Valid values: none

Show help message.

<input>
  • Valid values: filename of an input file
  • Default: input

Input file (see input options).

Input file options

An option consist of a keyword and its arguments. Each option has to start on a new line. Keywords are case-insensitive, but their arguments may be case-sensitive (e.g. filenames). Lines beginning with # are treated as comments and ignored.

Force field

AMBER and CHARMM force fields are supported:

  • For AMBER, parameters and system topology are specified with parmfile.
  • For CHARMM, parameters are specified with parameters and system topology is specified with structure.
parmfile
  • Valid values: filename of a PRMTOP file
  • Default: none

AMBER force field parameters and system topoloy.

parameters
  • Valid values: filename of a PRM file
  • Default: none

CHARMM force field parameters. The option can be specified more than once.

structure
  • Valid values: filename of a PSF file
  • Default: none

CHARMM system topology.

Iteractions

PME
  • Valid values: on, off
  • Default: on

Enable the particle-mesh Ewald summation for electrostatic interactions.

cutoff
  • Valid values: positive real number
  • Default: 9.0
  • Units: Angstrom

Cutoff distance for van der Waals interactions and real-space electrostatic interactions.

switching
  • Valid values: on, off
  • Default: on

Enable a switching function for van der Waals interactions.

switchDist
  • Valid values: positive real number
  • Default: 7.5
  • Units: Angstrom

Cutoff of the switching function.

implicit
  • Valid values: on, off
  • Default: off

Enable the implicit solvent (GBSA-OBC). Valid only for AMBER force field.

Restraints

atomRestraint / groupRestraint
  • Valid values: see bellow
  • Default: none

Supported restraints:

  • Individual atomic restraints (atomRestraint) apply a potential to each selected atom. The potential is centred at the reference coordinates of the specific atom.
  • Group-based atomic restraints (groupRestraint) apply a potential to each selected atom. The potential is centred at the centre of mass of the group.

A flat-bottom harmonic potential is used, where the force constants, widths, and axes can be specified. Also, the force constants can be time-dependent. The option can be specified more than once.

Syntax:

{atom|group}Restraint <selection>
    [fbRefCoor <filname>]
    [fbCentre <x> <y> <z> | fbCentreSel <centre selection>]
    [axes <axes>] [width <width>]
    [setpoints <k1>@<t1> [<k2>@<t2>] ...]
  • <selection>
    • Valid values: atom selection in VMD format
    • Default: none

    Atom selection upon which the restraint is be applied.

  • fbRefCoor
    • Valid values: filename of a PDB file
    • Default: none

    Reference coordinates. If fbRefCoor is not set, the initial coordinates are used.

  • fbCentre
    • Valid values: 3 real numbers
    • Default: none
    • Units: Angstrom

    Centre coordinates of the potential. If fbCentre is not set, the centre of mass of <selection> is used. This option is only usable with groupRestraint.

    Example:

    fbCentre 10.0 -5.25 0.0
    
  • fbCentreSel
    • Valid values: atom selection in VMD format
    • Default: none

    Atom selection whose center of mass is used as the centre for the potential. If fbCentreSel is not set, the centre of mass of <selection> is used. This option is only usable with groupRestraints.

  • axes
    • Valid values: x, y, z, xy, xz, yz, xyz
    • Default: xyz

    Axes along which the restraint is applied.

  • width
    • Valid values: positive real number
    • Default: 0.0 for atomRestraint, the linear extent of the atom group + 4.0 Ang for groupRestraint.
    • Units: Angstrom

    Width of the flat-bottom part of the potential.

  • setpoints
    • Valid values: List of k@t
    • Default: none
    • Units: k in kcal/mol/Ang^2, t in simulations steps or time units (see bellow)

    List of force constants at given time points. Each point (k@t) define is defined by the force constant (k) and time (t). The time can be specified in simulation steps or time using suffices (us, ns, ps, and fs). The force constant is interpolated linearly between the points.

    Example: at the beginning, the force constant is 10 kcal/mol/Ang^2 and reduces to 0 at 100 ns:

    setpoints 10@0ns 0@100ns
    

Examples:

  • Restrain all carbon-alpha atoms of the protein to their initial coordinates with the force constant of 5 kcal/mol/Ang^2:

    atomRestraint "protein and name CA" setpoints 5@0
    
  • Set the width of the flat-bottom harmonic potential to 2 Ang:

    atomRestraint "protein and name CA" width 2 setpoints 5@0
    
  • Apply restrain only along x and y axes:

    atomRestraint "protein and name CA" axes xy width 2 setpoints 5@0
    
  • Linearly decrease the force constant to 2 kcal/mol/Ang^2 from 0 to 10 ns, then keep it steady from 10 to 20 ns, and decrease to 0 from 20 to 30 ns:

    atomRestraint "protein and name CA" axes xy width 2 setpoints 5@0 2@10ns 2@20ns 0@30ns
    
  • Apply a group restraint to residue “LIG”, the potential is centered at the centre of mass of “LIG” using its initial position:

    groupRestraint "resname LIG" setpoints 5@0
    
  • Apply the potential centred at a specific position:

    groupRestraint "resname LIG" fbCentre 15.0 8.2 -7.3 setpoints 5@0
    
  • Apply the potential centred at the centre of mass of a protein:

    groupRestraint "resname LIG" fbCentreSel "protein" setpoints 5@0
    

Initial state

coordinates
  • Valid values: filename of a PDB file
  • Default: structure.pdb

Initial system coordinates.

binCoordinates
  • Valid values: filename of a NAMD BINCOOR file
  • Default: none

Initial system coordinates. If specified, overrides the initial coordinates from coordinates.

cellDimension
  • Valid values: 3 positive real numbers
  • Default: none
  • Units: Angstrom

Initial sizes of a simulation box.

Example:

celldimension 10.0 25.0 30.0
extendedSystem
  • Valid values: filename of a NAMD XSC file
  • Default: none

Initial sizes of a simulation box. Note that the simulation box has to be rectangular. If extendedSystem is set, it overrides cellDimension.

temperature
  • Valid values: positive real number
  • Default: 0.0
  • Units: Kelvin

Temperature for the generation of initial system velocities.

velocities
  • Valid values: filename of PDB file
  • Default: none

Initial system velocities. If velocities is set, it overrides the generated velocities.

binVelocities
  • Valid values: filename of a NAMD BINCOOR file
  • Default: none

Initial system velocities. If binVelocities is set, it overrides the initial velocities from velocities.

restart
  • Valid values: on, off
  • Default: off

Enable the restart of simulation from restart.chk file. The restart overrides the initial system coordinates, velocities, and sizes of the simulation box. Note that restart.chk is always written every trajectoryFreq steps irrespective of this option.

Minimization

minimize
  • Valid values: non-negative integer
  • Default: 0
  • Units: steps

Number of system minimization steps before starting a simulation. Note that the minimization is skipped if the simulation is restarted.

Integrator

run
  • Valid values: non-negative integer
  • Default: 0
  • Units: simulations steps or time units (see bellow)

Lenght of simulations. The length can be specified in simulation steps or time using suffices (us, ns, ps, and fs).

Example:

run 100ns
timestep
  • Valid values: positive real number
  • Default: 4.0
  • Units: fs

Time step of an integrator. Note that the constraints and hydrogen mass repartitioning is enabled automatically:

  • If timestep > 0.5 fs, enable hydrogen bond constraints and make water molecules rigid.
  • If timestep > 2.0 fs, enable all bond constraints and repartition hydrogen mass to 4.0 au.

Thermostat

thermostat
  • Valid values: on, off
  • Default: off

Enable Langevin thermostat.

thermostatTemp
  • Valid values: non-negative real number
  • Default: 300.0
  • Units: Kelvin

Target temperature for the thermostat

thermostatDamping
  • Valid values: non-negative real number
  • Default: 0.1
  • Units: ps^-1

Damping constant of the thermostat.

Barostat

barostat
  • Valid values: on, off
  • Default: off

Enable Monte Carlo barostat.

barostatPressure
  • Valid values: real number
  • Default: 1.0
  • Units: bar

Target pressure of the barostat.

useFlexibleCell
  • Valid values: on, off
  • Default: off

Enable the axes (x, y, z) of the simulation box to vary independently.

useConstantArea
  • Valid values: on, off
  • Default: off

Enable a constraint of x * y, while z varies independently.

useConstantRatio
  • Valid values: on, off
  • Default: off

Enable a constraint of x / y, while z varies independently.

Output

Final system coordinates, velocities, and sizes of the simulation box are always written to output.coor, output.vel and output.xsc, respectively.

trajectoryFile
  • Valid values: filename
  • Default: output.xtc

Trajectory in XTC format.

trajectoryFreq
  • Valid values: non-negative integer
  • Default: 25000
  • Units: simulation steps

Period of trajectory file. Note that the log and restart files are written at the same period.