Automate PLUMED metadynamics setup and analysis for free-energy landscapes.
npx skills add https://github.com/BioKT/Skills-BIOKT --skill plumed-metad
Please help me install this Agent Skill. Skill: plumed-metad Source: https://github.com/BioKT/Skills-BIOKT/tree/main/plumed-metad Command: npx skills add https://github.com/BioKT/Skills-BIOKT --skill plumed-metad
Automates PLUMED metadynamics workflow setup and analysis to map free-energy landscapes.
Begin with an unbiased MD run to estimate the CV sigma, then perform staged metadynamics using the provided templates to generate HILLS files and produce the FES data.
High-intent search queries and answers about installing and using this skill.
Set up a PLUMED metadynamics workflow by running an unbiased simulation to estimate CV sigma, then using the Stage 1–6 templates to configure bias deposition, reweighting, and convergence diagnostics for FES production.
Reweighting in metadynamics projects biased trajectories onto unbiased CV spaces using the Stage 4 workflow templates, allowing you to recover the unbiased free-energy landscape from your biased simulation data.
Yes, you need a GROMACS and PLUMED installation, along with user-supplied CV definitions, reference structures, temperature, and bias factors to generate input files and perform the staged simulations.
Assess convergence and estimate errors in metadynamics free-energy calculations by comparing FES evolution across snapshots using block analysis, which provides block-averaged error estimation during the convergence assessment stage.
Select collective variables by first running an unbiased simulation to determine CV fluctuations and range, which provides the sigma estimation needed to configure the bias deposition for your specific system.
BioKTCoordinate PLUMED multi-replica simulations for GROMACS umbrella sampling and metadynamics.
BioKTRun umbrella sampling workflows with PLUMED and GROMACS, including WHAM reweighting and free-energy surface construction.
RamanEbrahimiAutomate molecular dynamics simulations and trajectory analysis with OpenMM and MDAnalysis.
jpfieldingQuery IEA API endpoints for global energy statistics via curl.
