COMBINE

This is part of the function module

Calculate a polynomial combination of a set of other variables.

The functional form of this function is

\[ C=\sum_{i=1}^{N_{arg}} c_i (x_i-a_i)^{p_i} \]

The coefficients c, the parameters a and the powers p are provided as vectors.

Notice that COMBINE is not able to predict which will be periodic domain of the computed value automatically. The user is thus forced to specify it explicitly. Use PERIODIC=NO if the resulting variable is not periodic, and PERIODIC=A,B where A and B are the two boundaries if the resulting variable is periodic.

Examples

The following input tells plumed to print the distance between atoms 3 and 5 its square (as computed from the x,y,z components) and the distance again as computed from the square root of the square.

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

contract shortcuts

dist: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=3,5 
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x, 
 The DISTANCE action with label dist calculates the following quantities:

 Quantity   
 Description  
dist.x
the x-component of the vector connecting the two atoms
dist.y
the y-component of the vector connecting the two atoms
dist.z
the z-component of the vector connecting the two atoms


distance2: COMBINE 
ARG
the input to this function. 
=dist.x,dist.y,dist.z 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE action with label distance2 calculates a single scalar value
distance: COMBINE 
ARG
the input to this function. 
=distance2 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=0.5 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE action with label distance calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=distance,distance2 The PRINT action with label 

dist: DISTANCE 
ATOMS
the pair of atom that we are calculating the distance between. 
=3,5 
COMPONENTS
( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x, 
 The DISTANCE action with label dist calculates the following quantities:

 Quantity   
 Description  
dist.x
the x-component of the vector connecting the two atoms
dist.y
the y-component of the vector connecting the two atoms
dist.z
the z-component of the vector connecting the two atoms


distance2: COMBINE_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=dist.x,dist.y,dist.z 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=2,2,2 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE_SCALAR action with label distance2 calculates a single scalar value
distance: COMBINE_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=distance2 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=0.5 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=NO The COMBINE_SCALAR action with label distance calculates a single scalar value
PRINT 
ARG
the input for this action is the scalar output from one or more other actions. 
=distance,distance2 The PRINT action with label 

(See also PRINT and DISTANCE).

The following input tells plumed to add a restraint on the cube of a dihedral angle. Notice that since the angle has a periodic domain -pi,pi its cube has a domain -pi**3,pi**3.

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

contract shortcuts

t: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=1,3,5,7 The TORSION action with label t calculates a single scalar value
c: COMBINE 
ARG
the input to this function. 
=t 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=3 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=-31.0062766802998,31.0062766802998 The COMBINE action with label c calculates a single scalar value
RESTRAINT 
ARG
the arguments on which the bias is acting. 
=c 
KAPPA
compulsory keyword ( default=0.0 )
specifies that the restraint is harmonic and what the values of the force constants
on each of the variables are 
=10 
AT
compulsory keyword 
the position of the restraint 
=0 The RESTRAINT action with label 

t: TORSION 
ATOMS
the four atoms involved in the torsional angle 
=1,3,5,7 The TORSION action with label t calculates a single scalar value
c: COMBINE_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=t 
POWERS
compulsory keyword ( default=1.0 )
the powers to which you are raising each of the arguments in your function 
=3 
PERIODIC
compulsory keyword 
if the output of your function is periodic then you should specify the periodicity
of the function. 
=-31.0062766802998,31.0062766802998 The COMBINE_SCALAR action with label c calculates a single scalar value
@4: RESTRAINT_SCALAR 
ARG
the input for this action is the scalar output from one or more other actions. 
=c 
KAPPA
compulsory keyword ( default=0.0 )
specifies that the restraint is harmonic and what the values of the force constants
on each of the variables are 
=10 
AT
compulsory keyword 
the position of the restraint 
=0 The RESTRAINT_SCALAR action with label @4 calculates the following quantities:

 Quantity   
 Description  
@4.bias
the instantaneous value of the bias potential
@4.force2
the instantaneous value of the squared force due to this bias potential

Glossary of keywords and components

Compulsory keywords

PERIODIC	if the output of your function is periodic then you should specify the periodicity of the function. If the output is not periodic you must state this using PERIODIC=NO
COEFFICIENTS	( default=1.0 ) the coefficients of the arguments in your function
PARAMETERS	( default=0.0 ) the parameters of the arguments in your function
POWERS	( default=1.0 ) the powers to which you are raising each of the arguments in your function

Options

NORMALIZE	( default=off ) normalize all the coefficients so that in total they are equal to one
ARG	the input to this function. You can use multiple instances of this keyword i.e. ARG1, ARG2, ARG3...