MOVINGRESTRAINT

This is part of the bias module |

Add a time-dependent, harmonic restraint on one or more variables.

This form of bias can be used to performed steered MD [59] and Jarzynski sampling [74].

The harmonic restraint on your system is given by:

\[ V(\vec{s},t) = \frac{1}{2} \kappa(t) ( \vec{s} - \vec{s}_0(t) )^2 \]

The time dependence of \(\kappa\) and \(\vec{s}_0\) are specified by a list of STEP, KAPPA and AT keywords. These keywords tell plumed what values \(\kappa\) and \(\vec{s}_0\) should have at the time specified by the corresponding STEP keyword. In between these times the values of \(\kappa\) and \(\vec{s}_0\) are linearly interpolated.

Additional material and examples can be also found in the tutorial Belfast tutorial: Out of equilibrium dynamics

- Examples

The following input is dragging the distance between atoms 2 and 4 from 1 to 2 in the first 1000 steps, then back in the next 1000 steps. In the following 500 steps the restraint is progressively switched off.

Click on the labels of the actions for more information on what each action computes

d:DISTANCEATOMS=2,4 MOVINGRESTRAINT ...the pair of atom that we are calculating the distance between.ARG=the input for this action is the scalar output from one or more other actions.dSTEP0=0compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT0=1.0compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.KAPPA0=100.0compulsory keywordKAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.STEP1=1000compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT1=2.0compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.STEP2=2000compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT2=1.0compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.STEP3=2500compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.KAPPA3=0.0 ...compulsory keywordKAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.

The following input is progressively building restraints distances between atoms 1 and 5 and between atoms 2 and 4 in the first 1000 steps. Afterwards, the restraint is kept static.

Click on the labels of the actions for more information on what each action computes

d1:DISTANCEATOMS=1,5the pair of atom that we are calculating the distance between.d2:DISTANCEATOMS=2,4 MOVINGRESTRAINT ...the pair of atom that we are calculating the distance between.ARG=the input for this action is the scalar output from one or more other actions.d1,d2STEP0=0compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT0=1.0,1.5compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.KAPPA0=0.0,0.0compulsory keywordKAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.STEP1=1000compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT1=1.0,1.5compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.KAPPA1=1.0,1.0 ...compulsory keywordKAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.

The following input is progressively bringing atoms 1 and 2 close to each other with an upper wall

Click on the labels of the actions for more information on what each action computes

d1:DISTANCEATOMS=1,2 MOVINGRESTRAINT ...the pair of atom that we are calculating the distance between.ARG=the input for this action is the scalar output from one or more other actions.d1VERSE=Ucompulsory keyword ( default=B )Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B)STEP0=0compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT0=1.0compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.KAPPA0=10.0compulsory keywordKAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.STEP1=1000compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT1=0.0 ...compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.

By default the Action is issuing some values which are the work on each degree of freedom, the center of the harmonic potential, the total bias deposited

(See also DISTANCE).

- Attention
- Work is not computed properly when KAPPA is time dependent.

- Glossary of keywords and components

- Description of components

By default this Action calculates the following quantities. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity | Description |

bias | the instantaneous value of the bias potential |

work | the total work performed changing this restraint |

force2 | the instantaneous value of the squared force due to this bias potential |

_cntr | one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with the arguments of the bias followed by the character string _cntr. These quantities give the instantaneous position of the center of the harmonic potential. |

_work | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _work. These quantities tell the user how much work has been done by the potential in dragging the system along the various colvar axis. |

_kappa | one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _kappa. These quantities tell the user the time dependent value of kappa. |

- Compulsory keywords

VERSE | ( default=B ) Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than the restraint or whether it is acting on both sides (B) |

STEP | This keyword appears multiple times as STEP \(x\) with x=0,1,2,...,n. Each value given represents the MD step at which the restraint parameters take the values KAPPA \(x\) and AT \(x\). You can use multiple instances of this keyword i.e. STEP1, STEP2, STEP3... |

AT | AT \(x\) is equal to the position of the restraint at time STEP \(x\). For intermediate times this parameter is linearly interpolated. If no AT \(x\) is specified for STEP \(x\) then the values of AT are kept constant during the interval of time between STEP \(x-1\) and STEP \(x\). You can use multiple instances of this keyword i.e. AT1, AT2, AT3... |

KAPPA | KAPPA \(x\) is equal to the value of the force constants at time STEP \(x\). For intermediate times this parameter is linearly interpolated. If no KAPPA \(x\) is specified for STEP \(x\) then the values of KAPPA \(x\) are kept constant during the interval of time between STEP \(x-1\) and STEP \(x\). You can use multiple instances of this keyword i.e. KAPPA1, KAPPA2, KAPPA3... |

- Options

NUMERICAL_DERIVATIVES | ( default=off ) calculate the derivatives for these quantities numerically |

ARG | the input for this action is the scalar output from one or more other actions. The particular scalars that you will use are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates a single scalar value. The value of this scalar is thus used as the input to this new action. If * or *.* appears the scalars calculated by all the proceeding actions in the input file are taken. Some actions have multi-component outputs and each component of the output has a specific label. For example a DISTANCE action labelled dist may have three components x, y and z. To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.More information on the referencing of Actions can be found in the section of the manual on the PLUMED Getting Started. Scalar values can also be referenced using POSIX regular expressions as detailed in the section on Regular Expressions. To use this feature you you must compile PLUMED with the appropriate flag. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3... |