Action: MOVINGRESTRAINT

Module	bias
Description	Usage
Add a time-dependent, harmonic restraint on one or more variables.

Details and examples

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

This form of bias can be used to perform the steered MD and Jarzynski sampling calculations that are discussed in the papers cited below.

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.

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

DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,4 LABELa label for the action so that its output can be referenced in the input to other actions=dThe DISTANCE action with label d calculates the following quantities: Quantity    Type    Description  
d scalar the DISTANCE between this pair of atoms
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
  ARGthe labels of the scalars on which the bias will act=d
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0    AT0ATx is equal to the position of the restraint at time STEPx=1.0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=100.0
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=1000 AT1ATx is equal to the position of the restraint at time STEPx=2.0
  STEP2This keyword appears multiple times as STEPx with x=0,1,2,=2000 AT2ATx is equal to the position of the restraint at time STEPx=1.0
  STEP3This keyword appears multiple times as STEPx with x=0,1,2,=2500         KAPPA3KAPPAx is equal to the value of the force constants at time STEPx=0.0
... MOVINGRESTRAINT

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

DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,5 LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=2,4 LABELa label for the action so that its output can be referenced in the input to other actions=d2The DISTANCE action with label d2 calculates the following quantities: Quantity    Type    Description  
d2 scalar the DISTANCE between this pair of atoms
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
  ARGthe labels of the scalars on which the bias will act=d1,d2
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0    AT0ATx is equal to the position of the restraint at time STEPx=1.0,1.5 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=0.0,0.0
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=1000 AT1ATx is equal to the position of the restraint at time STEPx=1.0,1.5 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=1.0,1.0
... MOVINGRESTRAINT

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

DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=1,2 LABELa label for the action so that its output can be referenced in the input to other actions=d1The DISTANCE action with label d1 calculates the following quantities: Quantity    Type    Description  
d1 scalar the DISTANCE between this pair of atoms
MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
  ARGthe labels of the scalars on which the bias will act=d1
  VERSE 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)=U
  STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0    AT0ATx is equal to the position of the restraint at time STEPx=1.0 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=10.0
  STEP1This keyword appears multiple times as STEPx with x=0,1,2,=1000 AT1ATx is equal to the position of the restraint at time STEPx=0.0
... MOVINGRESTRAINT

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).

Work is not computed properly when KAPPA is time dependent.

Input

The arguments that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
ARG	scalar	the labels of the scalars on which the bias will act

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name	Type	Description
bias	scalar	the instantaneous value of the bias potential
work	scalar	the total work performed changing this restraint
force2	scalar	the instantaneous value of the squared force due to this bias potential
_cntr	scalar	one or multiple instances of this quantity can be referenced elsewhere in the input file
_work	scalar	one or multiple instances of this quantity can be referenced elsewhere in the input file
_kappa	scalar	one or multiple instances of this quantity can be referenced elsewhere in the input file

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
ARG	input	none	the labels of the scalars on which the bias will act
VERSE	compulsory	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	compulsory	none	This keyword appears multiple times as STEPx with x=0,1,2,
AT	compulsory	none	ATx is equal to the position of the restraint at time STEPx
KAPPA	compulsory	none	KAPPAx is equal to the value of the force constants at time STEPx
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically

References

More information about how this action can be used is available in the following articles:

Quantity	Type	Description
d	scalar	the DISTANCE between this pair of atoms