Functions

When performing biased dynamics or analyzing a trajectory you may wish to analyze/bias the value of some function of a set of collective variables rather than the values of the collective variables directly. You can do this with PLUMED by using any one of the following list of functions.

Notice that in many functions you should explicitly say to PLUMED whether the result is a periodic variable or not using the keyword PERIODIC. This is crucial to allow a variable to be properly based. To know if a function is periodic of not you should answer to the following question:

• Can my function change with a discontinuity when I move my atoms in a continuous manner?

In case the answer is no, than you should use PERIODIC=NO. In case the answer is yes, then you should consider the following question:

• Are the values of the function at the discontinuity always the same or do they change?

In case the answer is that they are the same, you should use PERIODIC=A,B where A is the smallest value and B is the largest value. In case the answer is that the values at the discontinuity are not always the same, then you cannot construct a variable that can be biased with PLUMED. Consider the following examples:

Click on the labels of the actions for more information on what each action computes
t: TORSION ATOMSthe four atoms involved in the torsional angle =1,2,3,4
# When atoms are moved, t could jump suddenly from -pi to +pi
c: MATHEVAL ARGthe input for this action is the scalar output from one or more other actions. =t FUNCcompulsory keyword
the function you wish to evaluate =x*x*x PERIODICcompulsory keyword
if the output of your function is periodic then you should specify the periodicity
of the function. =-31.0062766802998,31.0062766802998
# When atoms are moved, c could jump suddenly from -pi**3 to +pi**3
# equivalently, we could have used:
# c: COMBINE ARG=t POWERS=3 PERIODIC=-31.0062766802998,31.0062766802998
# compute x/y/z components of the distance between atoms 1 and 10
d: DISTANCE ATOMSthe pair of atom that we are calculating the distance between. =1,10 COMPONENTS( default=off ) calculate the x, y and z components of the distance separately and
store them as label.x,
# make a new variable equal to d.z but with the correct periodicity
dz: COMBINE ARGthe input for this action is the scalar output from one or more other actions. =d.z PERIODICcompulsory keyword
if the output of your function is periodic then you should specify the periodicity
of the function. =-10,10
# here we assumed the system is in a orthorhombic box with z side = 20

 COMBINE Calculate a polynomial combination of a set of other variables. CUSTOM Calculate a combination of variables using a custom expression. ENSEMBLE Calculates the replica averaging of a collective variable over multiple replicas. FUNCPATHGENERAL This function calculates path collective variables (PCVs) using an arbitrary combination of collective variables (see [58]). FUNCPATHMSD This function calculates path collective variables. FUNCSUMHILLS This function is intended to be called by the command line tool sum_hills. It is meant to integrate a HILLS file or an HILLS file interpreted as a histogram in a variety of ways. It is, therefore, not expected that you use this during your dynamics (it will crash!) LOCALENSEMBLE Calculates the average over multiple arguments. MATHEVAL An alias to the CUSTOM function. PIECEWISE Compute a piece wise straight line through its arguments that passes through a set of ordered control points. SORT This function can be used to sort colvars according to their magnitudes. STATS Calculates statistical properties of a set of collective variables with respect to a set of reference values.

In addition to the keywords above, by enabling optional modules you can access to the following keywords:

 SELECT (from PLUMED-ISDB module) Selects an argument based on the value of a SELECTOR.