Machine for molecular dynamics calculation (supports double precision)

A customer involved in the research and development of adhesive materials asked us about a machine for conducting large-scale molecular dynamics calculations.
We mainly use LAMMPS and GROMACS, and we plan to use quantum chemical calculations (Density Functional Theory: DFT) as necessary.
Also, in order to perform calculations with GPGPU, we also requested the installation of CUDA.

The specific conditions are as follows.

・The model is Mac Pro
・CPU: AMD ThreadripperPRO 3995WX 2.7GHz 64 cores
・ Memory: 256GB
・Storage: 480GB SSD S-ATA / 4TB HDD S-ATA
・Case: Tower type
・OS: Redhat series
・Other: CUDA Toolkit
・Budget: About 600 million yen

Based on the above, we have proposed the following specifications.

【Main Specifications】

CPU AMD Ryzen ThreadripperPRO 5995WX (2.70GHz 64 cores)
memory 256GB
Storage 1 480GB SSD S-ATA
Storage 2 4TB HDD S-ATA
video Nvidia T400
network on board (1GbE x1 10GBase-T x1)
Housing + power supply Tower type chassis + 1000W (redundant power supply)
OS Rocky Linux
Others CUDA Toolkit

This configuration assumes large-scale molecular dynamics calculations with LAMMPS and GROMACS.
The points to consider are as follows.

■ Points

Cooling method needs to be considered for configurations with AMD ThreadripperPRO and NVIDIA A100

Since AMD ThreadripperPRO comes standard with a water-cooled CPU cooler, the chassis side does not come standard with a fan that can cool the NVIDIA A100.Therefore, the cooling of the NVIDIA A100 is supported by adding a case fan dedicated to GPU cooling.Also, by attaching a dummy cover to the empty PCI-E slot, we are trying to improve the cooling efficiency of the NVIDIA A100.

When using LAMMPS and GROMACS, if you do not perform double precision calculations on the GPU, you can reduce the cost by changing the GPU to a general product.

The configuration of this case study is based on the conditions given by the customer.
Please feel free to contact us even if you are considering different conditions from what is posted.


・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 GROMACS?
GROMACS (Groningen Machine for Chemical Simulations) is a molecular dynamics simulation package developed at the University of Groningen in the Netherlands.It is primarily designed for biochemical molecules such as proteins, lipids and diffusion.

reference:GROMACS *Jumps to an external site


・What is NVIDIA A100?
The NVIDIA A100 is a high-end GPU designed with the Ampere architecture.It delivers up to 20x the performance compared to the previous generation.Suitable for various applications that require HPC, such as model training for complex AI learning that requires large-scale computing power and scalability, inference with Deep Learning, and double-precision simulation.

reference:NVIDIA A100 Tensor Core GPU (NVIDIA) *Jumps to an external site