Command Line Tools

PLUMED contains a number of simple command line tools. To use one of these tools you issue a command something like:

plumed <toolname> <list of input flags for that tool>

The following is a list of the various standalone tools that PLUMED contains.

benchmark benchmark is a lightweight reimplementation of driver focused on running benchmarks
completion Dumps the body of a bash function to be used for auto completion.
config inquire plumed about how it was configure
driver driver is a tool that allows one to to use plumed to post-process an existing trajectory.
driver-float Equivalent to driver, but using single precision reals.
gen_example gen_example is a tool that you can use to construct an example for the manual that users can interact with to understand
gen_json gen_json constructs a json file that includes a dictionary of actions, the keywords for those actions and the components and outputs this to standard output
gentemplate gentemplate is a tool that you can use to construct template inputs for the various actions
info This tool allows you to obtain information about your plumed version
kt Print out the value of \(k_BT\) at a particular temperature
manual manual is a tool that you can use to construct the manual page fora particular action
mklib compile one or more *.cpp files into a shared library you can create and export the variable PLUMED_MKLIB_CFLAGS with some extra compile time flags to be used you can create and export the variable PLUMED_MKLIB_LDFLAGS with some extra link time flags (and libraries) to be used
newcv create a new collective variable from a template
partial_tempering scale parameters in a gromacs topology to implement solute or partial tempering
patch patch an MD engine
pathtools pathtools can be used to construct paths from pdb data
pdbrenumber Modify atom numbers in a PDB, possibly using hybrid-36 coding.
pesmd Pesmd allows one to do (biased) Langevin dynamics on a two-dimensional potential energy surface.
selector create lists of serial atom numbers
simplemd simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms.
sum_hills sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file
vim2html convert plumed input file to colored html using vim syntax

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

drr_tool (from Extended-System Adaptive Biasing Force module) - Extract .grad and .count files from the binary output .drrstate - Merge windows
ves_md_linearexpansion (from Variationally Enhanced Sampling (VES code) module) Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion.

For all these tools and to use PLUMED as a plugin in an MD calculation you will need an input file.