Bio Mega Server

Dashboard Workspace Tools Jobs

GPU backend: Boltz-2 submits through the Slurm/Singularity runner adapter. Other tools stay visible until their adapters are configured.

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Molecular Dynamics

OpenMM MD

PaperCodeProduction Ready

Simulate protein only or protein-ligand interactions using AMBER force field

Details Paper Code

Job Name

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EXAMPLES

Task *Protein PDB FileEnter PDB CodeComplex PDB FileLigand CodeLigand SDF

Minimization Steps *Equilibration Time (ns) *Production Time (ns) *

Integration TimestepTemperature (Equilibration)Pressure (Equilibration)

This local OpenMM MD entry mirrors Tamarind's md-openmm tool.

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass
Storage: <5
Strategy: validated; shared system OpenMM runtime
Next: Expose timestep/steps/temperature controls and add storage quotas for longer trajectories.

OpenMM MD adapter ran real 1CRN benchmark via Slurm job 233 in 0.560s and produced final PDB, DCD trajectory, state_data.csv, and summary artifacts.

GROMACS

Simulate protein only or protein-ligand interactions using GROMACS force field

Molecular Dynamics

Membrane Protein MD (GROMACS)

Simulate membrane proteins embedded in lipid bilayers using GROMACS with CHARMM36 force field

Molecular Dynamics

BioEmu

Approximate equilibrium distribution

Molecular Dynamics

MM/GB(PB)SA

Calculate protein-ligand or protein-protein binding free energy using Molecular mechanics/Generalized-Born (Poisson-Boltzmann) surface area

Molecular Dynamics

Relative Binding Free Energy

Relative energy of protein-ligand complexes

Molecular Dynamics