PLUMED can be used to analyse trajectories either on the fly during an MD run or via postprocessing a trajectory using driver. About the simplest form of analysis that PLUMED can perform involves printing information to a file. PLUMED can output various different kinds of information to files as described below:

COMMITTOR	Does a committor analysis.
DUMPATOMS	Dump selected atoms on a file.
DUMPDERIVATIVES	Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
DUMPFORCES	Dump the force acting on one of a values in a file.
DUMPMASSCHARGE	Dump masses and charges on a selected file.
DUMPMULTICOLVAR	Dump atom positions and multicolvar on a file.
DUMPPROJECTIONS	Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).
PRINT	Print quantities to a file.
UPDATE_IF	Conditional update of other actions.

The UPDATE_IF action allows you to do more complex things using the above print commands. As detailed in the documentation for UPDATE_IF when you put any of the above actions within an UPDATE_IF block then data will only be output to the file if colvars are within particular ranges. In other words, the above printing commands, in tandem with UPDATE_IF, allow you to identify the frames in your trajectory that satisfy some particular criteria and output information on those frames only.

Another useful command is the COMMITTOR command. This command can only be used when running an molecular dynamics trajectory - it cannot be used when analysing a trajectory using driver. As detailed in the documentation for COMMITTOR this command tells PLUMED (and the underlying MD code) to stop the calculation one some criteria is satisified.

A number of more complicated forms of analysis can be performed that take a number of frames from the trajectory as input. In all these commands the STRIDE keyword is used to tell PLUMED how frequently to collect data from the trajectory. In all these methods the output from the analysis is a form of enseble average. If you are running with a bias it is thus likely that you may want to reweight the trajectory frames in order to remove the effect the bias has on the static behavoir of the system. The following methods can thus be used to calculate weights for the various trajectory frames so that the final ensemble average is an average for the cannonical ensemble at the appropriate temperature.

REWEIGHT_BIAS	Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored
REWEIGHT_METAD	Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system.
REWEIGHT_TEMP	Calculate weights for ensemble averages allow for the computing of ensemble averages at temperatures lower/higher than that used in your original simulation.

You can then calculate ensemble averages using the following actions.

AVERAGE	Calculate the ensemble average of a collective variable
HISTOGRAM	Accumulate the average probability density along a few CVs from a trajectory.
MULTICOLVARDENS	Evaluate the average value of a multicolvar on a grid.

For many of the above commands data is accumulated on the grids. These grids can be further analysed using one of the actions detailed below at some time.

CONVERT_TO_FES	Convert a histogram, \(H(x)\), to a free energy surface using \(F(x) = -k_B T \ln H(x)\).
DUMPCUBE	Output a three dimensional grid using the Gaussian cube file format.
DUMPGRID	Output the function on the grid to a file with the PLUMED grid format.
FIND_CONTOUR	Find an isocontour in a smooth function.
FIND_CONTOUR_SURFACE	Find an isocontour by searching along either the x, y or z direction.
FIND_SPHERICAL_CONTOUR	Find an isocontour in a three dimensional grid by searching over a Fibonacci sphere.
FOURIER_TRANSFORM	Compute the Discrete Fourier Transform (DFT) by means of FFTW of data stored on a 2D grid.
GRID_TO_XYZ	Output the function on the grid to an xyz file
INTEGRATE_GRID	Calculate the total integral of the function on the input grid
INTERPOLATE_GRID	Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing.

As an example the following set of commands instructs PLUMED to calculate the distance between atoms 1 and 2 for every 5th frame in the trajectory and to accumulate a histogram from this data which will be output every 100 steps (i.e. when 20 distances have been added to the histogram).

x: DISTANCE ATOMS=1,2
h: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1 STRIDE=5
DUMPGRID GRID=h FILE=histo STRIDE=100

It is important to note when using commands such as the above the first frame in the trajectory is assumed to be the initial configuration that was input to the MD code. It is thus ignored. Furthermore, if you are running with driver and you would like to analyse the whole trajectory (without specifying its length) and then print the result you simply call DUMPGRID (or any of the commands above) without a STRIDE keyword as shown in the example below.

x: DISTANCE ATOMS=1,2
h: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1 STRIDE=5
DUMPGRID GRID=h FILE=histo

Please note that even with this calculation the first frame in the trajectory is ignored when computing the histogram.

Notice that all the commands for calculating smooth functions described above calculate some sort of average. There are two ways that you may wish to average the data in your trajectory:

You might want to calculate block averages in which the first \(N\)N frames in your trajectory are averaged separately to the second block of \(N\) frames. If this is the case you should use the keyword CLEAR in the input to the action that calculates the smooth function. This keyword is used to specify how frequently you are clearing the stored data.
You might want to calculate an accumulate an average over the whole trajectory and output the average accumulated at step \(N\), step \(2N\)... This is what PLUMED does by default so you do not need to use CLEAR in this case.

Dimensionality Reduction

The remainder of the analysis tools within PLUMED allow one to do some form of dimensionality reduction as detailed below.

CLASSICAL_MDS	Create a low-dimensional projection of a trajectory using the classical multidimensionalscaling algorithm.
PCA	Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input.

As with the grids described previously the STRIDE keyword tells PLUMED how frequently to collect data from the trajectory. The RUN keyword then tells PLUMED how frequently to do the dimensionality reduction. As described above if RUN is not present and you are analysing trajectories using driver all the data in the traejctory (with the expection of the first frame) will be analysed.