For organizations
Create one governed application service for laboratories, engineering groups, and teaching environments on infrastructure your organization controls.
Software Marketplace
GROMACS
Molecular Dynamics
Available on request
High-throughput biomolecular dynamics for proteins, lipids, and nucleic acids, with replica ensembles and multi-node MPI for systems that need it.
MPI
Batch execution
Replica ensembles
A managed scientific-software service for your organization
Provide research and engineering teams with approved applications and reproducible execution without asking them or your infrastructure team to maintain every software stack.
What your users can do
Choose an available application, configure a simulation, submit and track the run, review logs and status, and retrieve the recorded results.
What your infrastructure team gets
Control approved applications and versions, licensing integration, access, resource quotas, execution policies, data location, and run history.
How WECORE deploys and operates it
We package and validate applications, deploy the service on your OpenStack infrastructure, integrate licenses where required, and provide ongoing operations.
Overview
Understanding GROMACS.
GROMACS is a molecular dynamics engine written for biomolecular systems and tuned for throughput.
Its non-bonded interaction routines are optimized for modern CPU architectures, while MPI supports systems that need more than one node.
Use cases
What people run it for.
Protein folding and conformational sampling
Run folding studies and conformational sampling long enough for the slow motions to show up.
Membranes and lipid bilayers
Prepare and equilibrate bilayer systems, then run membrane proteins in a realistic lipid environment.
Binding and free-energy perturbation
Estimate protein–ligand binding free energies from perturbation windows, each queued as an independent simulation.
Nucleic-acid dynamics and long production runs
Run nucleic-acid systems and the long production campaigns that ensemble methods depend on.
Run modes
How the application runs in a managed environment.
Managed batch execution
Replica ensembles at scale
Queue many independent replicas instead of one very large simulation; this is how most GROMACS workloads are structured. Multi-node MPI is also available for an individual system that genuinely needs it.
Managed batch execution
Single-node or multi-node MPI
Choose single-node execution for throughput or multi-node MPI when an individual system needs more memory or compute capacity.
Available on request
Run scientific software without managing the cluster.
Tell us which scientific application you need and how you plan to use it.