Run umbrella sampling workflows with PLUMED and GROMACS, including WHAM reweighting and free-energy surface construction.
npx skills add https://github.com/BioKT/Skills-BIOKT --skill plumed-us
Please help me install this Agent Skill. Skill: plumed-us Source: https://github.com/BioKT/Skills-BIOKT/tree/main/plumed-us Command: npx skills add https://github.com/BioKT/Skills-BIOKT --skill plumed-us
Umbrella sampling uses a series of harmonic restraint potentials (windows) to force the system to sample different regions along a reaction coordinate. The unbiased free energy is recovered by combining all windows via WHAM.
Define the collective variable and its range, generate the plumed window inputs, and run the umbrella sampling workflow to obtain WHAM-reweighted FES.
High-intent search queries and answers about installing and using this skill.
Umbrella sampling with PLUMED and GROMACS is performed by defining a collective variable, generating per-window restraint inputs, running multi-window simulations, and combining the results via WHAM to construct the reweighted free energy surface.
Collective variables for PLUMED umbrella sampling include distances, torsions, and RMSD. You define these CVs across a specified range to generate window inputs that drive the sampling and subsequent WHAM-based reweighting.
WHAM weights for molecular simulations are calculated by concatenating trajectories from per-window runs. The umbrella sampling workflow computes these weights to reweight the biased data and recover the unbiased free energy surface.
Yes, the umbrella sampling workflow supports serial and MPI or REMD execution across windows. It also includes optional replicas support to run multi-window simulations and concatenate trajectories for WHAM analysis.
Umbrella sampling convergence is validated using bootstrap-style error analysis alongside initial-condition checks. These steps ensure the WHAM-reweighted free energy surface is statistically reliable before finalizing the results.
Harmonic restraint potentials are needed for protein dynamics free energy calculations to force the system to sample different regions along a reaction coordinate. WHAM then combines these restrained windows to recover the unbiased free energy.
BioKTCoordinate PLUMED multi-replica simulations for GROMACS umbrella sampling and metadynamics.
LeonChaoXRun OpenMM molecular dynamics simulations and analyze trajectories with MDAnalysis.
BioKTAutomate PLUMED metadynamics setup and analysis for free-energy landscapes.
Lord1EgyptRun molecular dynamics simulations and analyze trajectories with OpenMM and MDAnalysis.
