Workstations for GROMACS and AMBER
GROMACS and AMBER run on the GPU, and most labs gain more from running several simulations at once than from splitting one across cards. We size these machines by how many runs you need in parallel.
What matters for GROMACS and AMBER
- One fast NVIDIA GPU per simulation
- More GPUs to run more simulations side by side
- A few CPU cores per GPU
- A full x16 PCIe slot for each GPU
- Linux, the best-tested platform
AMBER does not accelerate one simulation across several GPUs, but runs several simulations side by side with little or no slowdown (AMBER GPU hardware). GROMACS can split one simulation across GPUs, but a GROMACS developer reports no gain for small systems and only a modest gain from one GPU to two for large ones (GROMACS forum). So we scale by GPU count, one run per card. AMBER’s mixed precision means FP64 is not a constraint (AMBER GPU hardware). Up to four GPUs we use the NVIDIA RTX PRO 5000 48GB, with 48GB of ECC memory and 1,344 GB/s of bandwidth per card. AMBER needs at least one core per GPU and x16 slots, and GROMACS suggests one to three ranks per GPU (GROMACS performance guide). The Nano Pro gives each of its four GPUs a full PCIe Gen5 x16 link without riser cables. The eight-GPU Molecule Air takes the RTX PRO 6000 Max-Q only. GROMACS is best tested on Linux, so every build ships with Rocky Linux 9.
Recommended configurations
GROMACS and AMBER – Standard
Electron · NVIDIA RTX PRO 5000 48GB
For a single artist or engineer
- CPU: AMD Ryzen 9 9950X3D
- RAM: 128GB DDR5 6000 2x64GB
- PCIe slots (16x): Nvidia RTX Pro 5000 Blackwell 48GB
- NVMe Storage (Gen 5.0): Samsung 9100 Pro Gen 5 4TB
- Operating System: RBOS Rocky 9
£15,171.19 inc VAT
£12,642.66 ex VAT
Built to order · dispatched in 11 working days
GROMACS and AMBER – Heavy
Atom · 2× NVIDIA RTX PRO 5000 48GB
For professionals and freelancers
- CPU: AMD Ryzen Threadripper 9960X 24 Core
- RAM: 4 × 64GB RDIMM ECC DDR5 6400
- PCIe slots (16x): 2 × Nvidia RTX Pro 5000 Blackwell 48GB
- NVMe M.2 Drives (Gen 5): Samsung 9100 Pro Gen 5 4TB
- Operating System: RBOS Rocky 9
£35,171.00 inc VAT
£29,309.18 ex VAT
Built to order · dispatched in 11 working days
GROMACS and AMBER – Studio
Nano Pro · 4× NVIDIA RTX PRO 5000 48GB
For studios and small teams
- CPU: AMD Ryzen Threadripper PRO 9975WX 32 Core
- RAM: 8 × 64GB RDIMM ECC DDR5 6400
- PCIe Options: 4 × Nvidia RTX Pro 5000 Blackwell 48GB
- NVMe M.2 Drives (Gen 5): Samsung 9100 Pro Gen 5 8TB
- Operating System: RBOS Rocky 9
£73,040.68 inc VAT
£60,867.25 ex VAT
Built to order · dispatched in 12 working days
GROMACS and AMBER – Team
Molecule Air · 8× NVIDIA RTX PRO 6000 Max-Q 96GB
For large teams and enterprise
- CPU: AMD EPYC 9375F 32 Core
- RAM: 24 × 32GB RDIMM ECC DDR5 6400
- PCIe slots: 8 × Nvidia RTX Pro 6000 Blackwell Max-Q 96GB
- Operating System: RBOS Rocky 9
£193,683.02 inc VAT
£161,402.52 ex VAT
Built to order · dispatched in 14 working days
Each recommended system is a starting point. Select Customise to add components or change the specification before you order.
Tell us what you need for GROMACS and AMBER
Share your GROMACS or AMBER versions, typical system sizes and how many simulations you run at once. We will review the right configuration and confirm availability before you order.
Frequently asked questions
Usually not by much. AMBER does not accelerate one simulation across several GPUs (AMBER GPU hardware). GROMACS can, but a developer reports no gain for small systems and only a modest gain for large ones (GROMACS forum). Extra GPUs pay off by running more simulations at once.
AMBER’s mixed precision means FP64 is not a constraint (AMBER GPU hardware). Up to four GPUs we use the NVIDIA RTX PRO 5000 48GB, with 48GB of ECC memory per card. The eight-GPU Team build uses the RTX PRO 6000 Max-Q because that is the card the Molecule Air takes.
Rocky Linux 9. GROMACS GPU acceleration is tested on Linux and Windows, with Linux the best tested (GROMACS installation guide).
AMBER needs at least one core per GPU (AMBER GPU hardware). For GROMACS, one to three ranks per GPU is generally best, and one rank per GPU in GPU-resident mode (GROMACS performance guide). Every configuration here has several cores per GPU.
Choose by how many simulations you want to run at once: one on Standard, two on Heavy, four on Studio and eight on Team. Team also suits large GROMACS systems decomposed across GPUs.
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