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

GROMACS

PaperCodeProduction Ready

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

Details Paper Code

Job Name

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EXAMPLES

System Type *Upload TypePDB FilePDB IDProtein FileLigand File

Force Field *Simulation Box TypeWater ModelSalt Concentration (mol/L)Temperature (K)Pressure (bar)

Save Frequency (ps)NVT Equilibration Time (ns)NPT Equilibration Time (ns)Simulation Time (ns)Trajectory FormatNumber of Replicas

Readiness

Readiness: Production Ready
Smoke: passed
Artifacts: passed
Production: production_pass
Storage: <5
Strategy: validated; shared apt GROMACS 2023.3 CPU runtime
Next: Expose PDB upload, force field/water model, minimization steps, and later add solvated MD/NVT/NPT workflows.

GROMACS 2023.3 installed system-wide; real RCSB 1CRN workflow ran pdb2gmx, editconf, grompp, and mdrun energy minimization via Slurm job 236 in 1.581s with 23 artifacts. Installed Ubuntu build is CPU-only; GPU-optimized SIF/build can be added later.

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

Relative Binding Free Energy

Relative energy of protein-ligand complexes

Molecular Dynamics