Bio Mega Server

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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 Protein Relaxation

secondsPaperProduction Ready

Relax a protein structure using OpenMM

Job Name

Log in to submit jobs to the Slurm backend.

EXAMPLES

PDB File *

Tamarind API type: openmm-relax.

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass
Storage: <5
Strategy: validated; shared system OpenMM/PDBFixer runtime
Next: Expose PDB upload and minimization iteration controls; optional GPU/OpenCL/CUDA platform tuning later.

OpenMM 8.0 with PDBFixer installed on backend; real RCSB 1CRN minimization benchmark passed via Slurm job 232 in 0.391s with relaxed PDB, energy CSV, stdout/stderr 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

OpenMM MD

Simulate protein only or protein-ligand interactions using AMBER 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