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安裝中文字典英文字典辭典工具!
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- 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
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