What is PLUMED? | plumed by plumed What is PLUMED? PLUMED is an open-source, community-developed library that provides a wide range of different methods, which include: enhanced-sampling algorithms; free-energy methods; tools to analyze the vast amounts of data produced by molecular dynamics (MD) simulations
PLUMED: Introduction PLUMED is a plugin that works with a large number of molecular dynamics codes (Codes interfaced with PLUMED) It can be used to analyze features of the dynamics on-the-fly or to perform a wide variety of free energy methods
How to get PLUMED | plumed by plumed Conda-forge, packages plumed and py-plumed, as pre-compiled binaries with basic capabilities Other conda binaries containing development versions or nightly builds are available on the plumed channel
The PLUMED manual | plumed by plumed Here you can find the user manuals for currently supported and old versions of PLUMED, along with a manual of the PLUMED GitHub master branch (development version) Documentation for recent releases v2 9 x
PLUMED: Installation As of PLUMED 2 5 it is possible to use the PLUMED library through Python wrappers Notice that this is not something for end users but rather for developers The interface is very similar to the one used in MD codes linked with PLUMED
PLUMED User’s Guide 1 1 What is PLUMED? PLUMED[1] is a plugin for free-energy calculations in molecular systems It works with some of the most popular classical molecular dynamics (MD) codes, such as GROMACS [2], NAMD [3], DL POLY [4] , LAMMPS [5] and the SANDER module in AMBER [6] It also works with the very fast
Tutorials - PLUMED PLUMED Masterclass 22 13: SASA module and the application of PLUMED for implicit solvent simulations This Masterclass explains how to use the SASA module of PLUMED to perform implicit solvent simulations
Advanced Methods in MD 2023: Metadynamics simulations with PLUMED PLUMED can be used to compute collective variables (CVs) on a pre-calculated trajectory However, PLUMED is most often use to add forces on the CVs during a MD simulation, for example, in order to accelerate sampling To this aim, we have implemented a variety of possible biases acting on CVs
Belfast tutorial: Out of equilibrium dynamics - PLUMED In plumed you can bring a system in a specific state in a collective variable by means of the MOVINGRESTRAINT directive This directive is very flexible and allows for a programmed series moving restraints This technique can be used also to sample multiple events within a single simulation
UNITS - PLUMED A new unit can be set by either specifying a conversion factor from the plumed default unit or by using a string corresponding to one of the defined units given below This directive MUST appear at the BEGINNING of the plumed dat file