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:
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:
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:
t: TORSION ATOMS=1,2,3,4 # When atoms are moved, t could jump suddenly from -pi to +pi c: MATHEVAL ARG=t FUNC=x*x*x PERIODIC=-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 ATOMS=1,10 COMPONENTS # make a new variable equal to d.z but with the correct periodicity dz: COMBINE ARG=d.z PERIODIC=-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. |
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. |