Workstation for molecular dynamics calculations | TEGAKARI, an information dissemination media for research and development

A customer involved in mineralogy research looked at Case No. PC-12076C, PC-12076D, etc. and asked us about a calculator for DFT (density functional theory) and molecular dynamics calculations using Advance/NanoLabo.
Our customers have requested that they need around 100GB to 200GB of memory in order to handle DFT with around 128 to 256 atoms.
In addition to molecular dynamics calculations, they are requesting a computer configuration that can also handle the analysis of X-ray CT data acquired during Spring-8.

Based on the information you provided, we proposed the following configuration based on Case No. PC-12076D.

CPU	Intel Xeon W7-3555 2.70GHz (up to 3.0GHz at TB4.8) 28C/56T
memory	Total 256GB DDR5 5600 REG ECC 32GB x 8
storage	4TB HDD S-ATA
Video	NVIDIA RTX2000 Ada 16GB (MiniDisplayPort x 4)
network	on board (1GbE x 1 /10GbE x 1)
Housing + power supply	Tower type case 1000W 80PLUS PLATINUM
OS	Microsoft Windows 11 Professional 64bit

In the example shown here, the CPU has been changed from "Xeon W7-3455 (24 cores)" to the successor model "Xeon W7-3555 (28 cores)".
The Xeon W7-3555 has more cores than the Xeon W7-3455, improving multi-threaded performance and large-scale data processing efficiency. It delivers higher processing performance in high-load tasks, and you can expect improved overall work efficiency and responsiveness.
For the GPU used to analyze X-ray CT data, we chose the "RTX2000 Ada 16GB."

Number of memory cards installed

The CPU used this time, the Xeon W7-3555 (28 cores), supports 8 channels of memory.
To maximize the CPU performance,Each channel is equipped with one memory module, for a total of 1GB (256GB x 32 modules).
By installing memory according to the number of memory channels, data transfer between the CPU and memory is optimized, maximizing the bandwidth utilization.

Reference: Performance changes depending on memory configuration

In terms of expandability, the motherboard has eight available slots, so by adding 8GB modules of the same specifications, the memory capacity can be increased up to a total of 32GB (512GB x 32).

However, even if eight or more memory modules are installed, the number of buses (memory channels) between the CPU and memory does not increase, so the amount of data that can be exchanged simultaneously (bandwidth) remains unchanged, and no improvement in communication speed can be expected.
Please note that although memory capacity increases, it does not directly translate to processing speed..
*Memory speed is based on the CPU speed.

Reference: Intel® Xeon® w7-3555 processor *Jumps to an external site

It is important to flexibly review the memory configuration and other specifications depending on the purpose of use and processing content.
Please feel free to contact us even if your purpose or budget is different from what is listed.

Workstation including licenseIntroductionFor those considering

This configuration does not include the "Advance Nanolabo" license.

If you do not have a license or would like to set up an environment that includes software, we offer a one-stop service that covers everything from obtaining software licenses to selecting and setting up the optimal hardware.turnkey system” is also available.

Eliminate the hassle of installationAs soon as it arrivedWe provide an environment where you can begin your research.

If you are considering introducing our software, please feel free to contact us.

■ Keywords

・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

・What is Quantum Espresso?

Quantum Espresso is open source software written in Fortran95 and distributed free of charge under the GNU General Public License. First-principles electronic state calculation program. It is a first-principles calculation code based on density functional theory. It is capable of optimizing atomic positions and cell structures, calculating electronic states and band structures, analyzing phonon vibrations, and calculating neutron scattering. It operates on multiple platforms and supports parallelization using MPI and OpenMP. It is widely used for theoretical analysis of material properties and the search for new substances, and is also a useful tool in computational biology.