Coordinate PLUMED multi-replica simulations for GROMACS umbrella sampling and metadynamics.
npx skills add https://github.com/BioKT/Skills-BIOKT --skill plumed-remd
Please help me install this Agent Skill. Skill: plumed-remd Source: https://github.com/BioKT/Skills-BIOKT/tree/main/plumed-remd Command: npx skills add https://github.com/BioKT/Skills-BIOKT --skill plumed-remd
PLUMED multi-replica simulations enable efficient umbrella sampling, bias-exchange METAD, and parallel-tempering METAD, including demuxing trajectories and WHAM analysis, streamlining complex MD workflows across replicas.
Configure your PLUMED multi-replica setup and run mpiexec across all replica directories using the -plumed input and -replex settings.
High-intent search queries and answers about installing and using this skill.
You run PLUMED replica exchange with GROMACS using MPI-based orchestration, supplying -multidir, -replex, and -plumed inputs across replica directories to coordinate umbrella sampling and metadynamics efficiently.
Bias-exchange metadynamics uses multiple replicas exchanging biases to sample distinct collective variables, handled here through MPI orchestration, PLUMED integration, and input generation templates across replica directories.
Yes, you can demux trajectories to reconstruct continuous pathways and estimate unbiased populations using the included WHAM Python script, streamlining post-processing for umbrella sampling and metadynamics workflows.
Yes, parallel-tempering metadynamics is supported alongside bias-exchange METAD, US-REMD, and independent replicas, providing the necessary MPI orchestration and PLUMED integration templates.
You need PLUMED input files and replica directories configured for MPI execution, using the provided input generation templates to manage -plumed inputs and -replex settings via mpiexec.
BioKTAutomate GROMACS source installation with PLUMED patching and CUDA/MPI configuration.
BioKTRun umbrella sampling workflows with PLUMED and GROMACS, including WHAM reweighting and free-energy surface construction.
SciMate-AIAutomates end-to-end HPC GROMACS workflows from preprocessing to analysis.
swaruplabRun and analyze MD simulations with OpenMM and MDAnalysis for biomolecular dynamics.
