GROMACS/LAMMPS workstation

A client conducting molecular simulation research contacted us to inquire about installing a workstation that would use GROMACS and LAMMPS.
The client wanted hardware with two GPUs and IPMI functionality in a Linux OS environment, and was considering building a system that would include installation support and post-implementation maintenance.
In order to connect with internal PCs, we would like to ask for advice on network configuration, including SSH connections and IP address settings.

CPU	Intel Xeon W5-2565X 3.20GHz (up to 3.0GHz at TB4.8) 18C/36T
memory	Total 128GB DDR5 5600 REG ECC 32GB x 4
storage	2TB SSD M.2 NVMe Gen5
Video	NVIDIA RTX PRO4000 24GB
network	on board (1GbE x1 /10GbE x1)
Housing + power supply	Mid-tower case 1500W 80PLUS PLATINUM
OS	Ubuntu 24.04
Miscellaneous	5-year send-back warranty TEGARA LAMMPS setup TEGARA GROMACS Setup

CPU and memory configuration

The Xeon W5-2565X (18 cores) is used, ensuring the computational performance necessary for parallel computing such as GROMACS and LAMMPS.

The memory is 128GB (4 x 32GB), and can be expanded up to 256GB in the future.
This allows for large-scale molecular dynamics simulations.

GPU selection

The RTX 4000 Ada that was originally requested has been discontinued, so we changed the configuration to include two current RTX PRO 4000 (Blackwell generation) cards.
Both GPUs support PCI-E x16 lane connections, enabling both faster and more stable computing performance.

IPMI functionality and network configuration

The IPMI port is shared with the motherboard's 1GbE port, and the connectionRemote management possible.
However, if you use this 1GbE port as IPMI, only one LAN port (10GbE) can be used.
If you need to increase the number of ports, you can do so by adding a network card.
If you add a network card, you will not be able to install a third GPU, so please be aware of this if you are planning to add more GPUs.

We can also provide support regarding integration with in-house PCs, such as IP address settings and SSH connections.
You can choose to have the setup work done before delivery or on-site.
(Although there was a request for this project, installation support was ultimately not provided.)

Security and enclosure

During the interview process with the customer, they also consulted us about physical security, such as lockable racks.
In addition to workstations and servers, we also offer proposals for server racks (18U) and base plate options.
You can select the case that matches your desired rack type, and you can also select a case with a slot for a security lock cable.

For those who are active in these fields Computational science Molecular dynamics Materials science Bioinformatics theoretical physics

Tegara's custom-made PC production service not only caters to initial use, but also supports system expansion in anticipation of future expansion of research scale.
We not only propose configurations that meet various software requirements, but also accept consultations regarding the construction of an entire research environment.
Please feel free to contact us and we will provide the best solution to suit your needs.

Keyword ・What is GROMACS? GROMACS is open-source software that can quickly perform molecular dynamics simulations on a scale of hundreds of thousands to millions of atoms. It supports advanced parallel calculations using GPUs and multi-core CPUs, allowing it to efficiently perform large-scale, long-term analyses. It also supports a variety of force fields, including AMBER and CHARMM, allowing it to flexibly handle a wide range of molecular systems. Reference: GROMACS Official Website*Jumps to an external site ・What is LAMMPS? LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is an open-source molecular dynamics calculation application developed by Sandia National Laboratories in the United States.It has a reputation for its wide range and flexibility of force fields that can be handled by parameter settings. Reference: LAMMPS Molecular Dynamics Simulator*Jumps to an external site

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