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Manual#

Command line arguments#

Syntax:

acemd [--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:

acemd --device 0,2
--precision

  • Valid values: single, mixed, double

  • Default: mixed

Set the precision mode on GPU devices.

--licence

  • Valid values: none

Check the licence.

--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.

switchDistance

  • Valid values: positive real number

  • Default: 7.5

  • Units: Angstrom

Cutoff of the switching function.

implicitSolvent

  • 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>
    [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.

  • 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
fbRefCoor

  • Valid values: filename of a PDB file

  • Default: none

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

Metadynamics#

plumedFile

  • Valid values: filename of a PLUMED input file

  • Default: none

Enables PLUMED. It can be used to perform enhanced sampling simulations (i.e. metadynamics, steered MD, etc.) or apply complex restraints. For more details, see our metadynamics tutorial and PLUMED documentation.

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.

boxSize

  • Valid values: 3 positive real numbers

  • Default: none

  • Units: Angstrom

Initial sizes of a simulation box.

Example:

boxSize 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: 298.15

  • 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 box size. Also, the states of thermostat and barostart are overridden, if they are used. Note that restart.chk is always written every trajectoryPeriod steps irrespective of this option. Note that restart.chk can only be used to restart on the same hardware (i.e. a GPU has be of the same model).

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.

slowPeriod

  • Valid values: positive integer

  • Default: 1

Period of slow interactions for the integrator. The slow interactions (the reciprocal term of PME) are computed at every slowPeriod steps, while the fast interactions (all the terms except the reciprocal term of PME) are computed at every step. Also, the slow interactions are scaled by slowPeriod.

For example, if slowPeriod 2, the forces for the integrator are computed:

F = 2 * F_slow + F_fast   for even steps
F = F_fast                for odd steps

If slowPeriod 1, the fast and slow forces ara computed at every step:

F = F_slow + F_fast

Note that the energies in the log are always physical (E = E_slow + E_fast) regardless of the slowPeriod value.

Thermostat#

thermostat

  • Valid values: on, off

  • Default: off

Enable Langevin thermostat.

thermostatTemperature

  • Valid values: non-negative real number

  • Default: 298.15

  • 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.

barostatAnisotropic

  • Valid values: on, off

  • Default: off

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

barostatConstRatio

  • Valid values: on, off

  • Default: off

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

barostatConstXY

  • Valid values: on, off

  • Default: off

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

Output#

The final atomic positions, velocities, and sizes of the simulation box are always written to output.coor, output.vel and output.xsc, respectively.

trajectoryFile

  • Valid values: filename with a dcd or xtc extension

  • Default: output.xtc

Name of a trajectory file for atomic positions. The trajectory is written in DCD or XTC format depending on the file extension. The positions are in Å. By default, the atomic positions are not wrapped, unless the barostat is enabled. The atomic positions can be wrapped with moleculekit.

trajVelocityFile

  • Valid values: filename with a dcd extension

  • Default: none

Name of a trajectory file for atomic velocities. The trajectory is written in DCD format only. The velocities are in arbitrary units, which can be converted to Å/ps by multiplying by 20.45482706 (the standard of DCD).

trajForceFile

  • Valid values: filename with a dcd extension

  • Default: none

Name of a trajectory file for atomic forces. The trajectory is written in DCD format only. The forces are in kcal/mol/Å.

trajectoryPeriod

  • Valid values: non-negative integer

  • Default: 25000

  • Units: simulation steps

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

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