Introduction

In earlier versions of ACEMD applying restraining potentials to the system required TCL scripting. Starting from now, ACEMD3 has support for directly defining restraints without needing any scripting.

Two classes of restraint are currently supported:

  • Atom-centred Restraints defined with the command atomRestraint. These restraints apply a flat-bottomed harmonic potential to restrain individual atoms about a reference coordinate.
  • Group-based Restraints defined with the command groupRestraint. These restraints apply a flat-bottomed harmonic potential to restraint a group of atoms about a reference centre-of-mass coordinate.

Command Syntax

{atom,group}Restraint "[atom selection]" axes {xyz} width [l] setpoints [k@t] ...

atom selection

Each restraint type requires an atom selection (in VMD atom selection grammar) to define the atoms upon which the restraint will be applied. The selection also defines the reference coordinates for the restraint, made against the geometry in the coordinates PDB file.

  • For an atomRestraint, each individual atom in the selection is restrained about its initial coordinate in the PDB by a flat-bottomed harmonic potential.
  • For a groupRestraint, the atoms in the selection are restrained about their centre of mass in the initial PDB by a flat-bottomed harmonic potential.

axes

Specifies the axes along which the restraint will apply. The default is “xyz”, indicating a 3D restraint. To apply a restraint solely in the Z direction, allowing particles to diffuse freely in an X-Y plane, use “axes z”.

This keyword is optional. If omitted the “xyz” default is used.

width

Specifies the width of the flat bottom of the restraining potential in Angstrom. When set the same width is applied to each dimension that the restraint is active for (see axes).

This keyword is optional. If omitted, the default is used:

  • For an atomRestraint, the default value is 0.
  • For a groupRestraint, the default value is the linear extent of the atom selection plus 4 Angstroms.

setpoints

These define the spring constant __k__ for the restraint at time __t__. When multiple setpoints are defined, ACEMD3 will linearly ramp __k__ between them, at trajectoryFreq intervals.

The syntax is k@t, where k is in kcal/mol and ‘t’ is in number of steps or in time if one of the suffices ‘us’, ‘ns’, ‘ps’, ‘fs’ is used.

For example, a 10 kcal/mol restraint applied from the beginning of the simulation, gradually reduced to 0 at 100ns may be defined with:

setpoints 10@0ns 0@100ns