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.

 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 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 a .cpp file into a shared library 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.