Module: generic

Description	Usage
generic features of PLUMED many of which are for printing data to files
Authors: The PLUMED core developers

Details

This module contains a range of generic PLUMED actions that can be used in many different types of calculation. For example, many of the commands in this module are used to print data that has been calculated by PLUMED to files.

This module also contains functionalities such as WHOLEMOLECULES or WRAPAROUND that can be used to manipulate the positions that are passed from the MD code to PLUMED. Additionally, this module contains features such as CONSTANT and PDB2CONSTANT that can be used to store constant values.

The last set of featuers in this module are COLLECT, ACCUMULATE, AVERAGE and GATHER_REPLICAS that can be used to gather data from multiple frames in the trajectory or from multiple replicas for further analysis.

References

More information about this module is available in the following articles:

• G. A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni, G. Bussi, PLUMED 2: New feathers for an old bird. Computer Physics Communications. 185, 604–613 (2014)

Actions

The following actions are part of this module

GENERIC: generic actions for printing and so on GRIDCALC: actions that output a function computed on a grid COLVAR: a function of a set of atomic positions that returns a scalar TOPOLOGY: actions for providing information on the molecular topology ANALYSIS: tools for analysing trajectories PRINTANALYSIS: tools for printing data that was obtained from an analysis of multiple frames of the trajectory DIMRED: dimensionality reduction algorithms

Name	Description	Tags
ACCUMULATE	Sum the elements of this value over the course of the trajectory	GRIDCALC
AVERAGE	Calculate the ensemble average of a collective variable	GRIDCALC
COLLECT	Collect data from the trajectory for later analysis	ANALYSIS
COMMITTOR	Does a committor analysis.	PRINTANALYSIS
CONSTANT	Create a constant value that can be passed to actions	COLVAR
CREATE_MASK	Create a mask vector to use for landmark selection	DIMRED
DEBUG	Set some debug options.	GENERIC
DUMPATOMS	Dump selected atoms on a file.	PRINTANALYSIS
DUMPDERIVATIVES	Dump the derivatives with respect to the input parameters for scalar values (generally CVs, functions or biases).	PRINTANALYSIS
DUMPFORCES	Dump the force acting on one of a values in a file.	PRINTANALYSIS
DUMPMASSCHARGE	Dump masses and charges on a selected file.	PRINTANALYSIS
DUMPPDB	Output PDB file.	PRINTANALYSIS
DUMPPROJECTIONS	Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).	PRINTANALYSIS
DUMPVECTOR	Print a vector to a file	PRINTANALYSIS
EFFECTIVE_ENERGY_DRIFT	Print the effective energy drift	GENERIC
ENDPLUMED	Terminate plumed input.	GENERIC
FIT_TO_TEMPLATE	This action is used to align a molecule to a template.	GENERIC
FLUSH	This command instructs plumed to flush all the open files with a user specified frequency.	GENERIC
GATHER_REPLICAS	Create a vector that contains the copies of the input quantities from all replicas	ANALYSIS
INCLUDE	Includes an external input file, similar to #include in C preprocessor.	GENERIC
MOLINFO	This command is used to provide information on the molecules that are present in your system.	TOPOLOGY
ONES	Create a constant vector with all elements equal to one	COLVAR
PDB2CONSTANT	Create a constant value from a PDB input file	COLVAR
PLUMED	Embed a separate PLUMED instance.	GENERIC
PRINT	Print quantities to a file.	PRINTANALYSIS
PRINT_NDX	Print an ndx file	PRINTANALYSIS
RANDOM_EXCHANGES	Set random pattern for exchanges.	GENERIC
READ	Read quantities from a colvar file.	GENERIC
READMASSCHARGE	Set the masses and charges from an input PDB file.	COLVAR
RESET_CELL	This action is used to rotate the full cell	GENERIC
TIME	retrieve the time of the simulation to be used elsewhere	GENERIC
UPDATE_IF	Conditional update of other actions.	PRINTANALYSIS
WHOLEMOLECULES	This action is used to rebuild molecules that can become split by the periodic boundary conditions.	GENERIC
WRAPAROUND	Rebuild periodic boundary conditions around chosen atoms.	GENERIC