Autodock Vina/GROMACS workstation

A customer involved in pharmaceutical research contacted us with a question about introducing a PC for molecular simulation.
The software they plan to use is Autodock Vina (or vina-gpu) and GROMACS, the OS they want is Ubuntu, and they are mainly considering Intel Core CPUs, but are also comparing AMD Ryzen configurations as options.
The base memory is 32GB, and the customer would like to confirm the degree of performance improvement that would result from upgrading to 64GB.

CPU	AMD Ryzen9 9950X3D 4.30GHz (up to 5.70GHz at Boost) 16C/32T
memory	Total 32GB DDR5 5600 16GB x 2
Storage 1	1TB SSD S-ATA
Video	NVIDIA GeForce RTX5070 12GB
network	on board(2.5G x1) Wi-Fi, Bluetooth
Housing + power supply	Mid-tower chassis + 1000W 80PLUS PLATINUM
OS	Ubuntu 24.04

About CPU

In this configuration,AMD Ryzen 9 9950X3DWas adopted.
GROMACS makes extensive use of the CPU's L3 cache.Cache capacity has a significant impact on processing performance international success.
Ryzen 9 9950X3D128MBIt has an L3 cache of 1.0, and the GROMACS benchmark on OpenBenchmarking.org showsHigh processing performance recordeddoing.

Reference: GROMACS Benchmark – OpenBenchmarking.org

Therefore, we adopted this configuration to maximize the computational efficiency for molecular simulation applications.
On the other hand, if you prefer the Intel Core Ultra series due to compatibility with your existing operating environment or cost considerations, we can also propose a configuration based on that.
We will guide you to the best environment depending on your needs and requirements.

GPU selection

For GPUsNVIDIA GeForce RTX 5070is selected.
The software we plan to use, vina-gpu and GROMACS, supports computational acceleration using CUDA-enabled GPUs, and the RTX 5070 meets these requirements.
Stable operation in an Ubuntu environment has also been confirmed, making it suitable for configurations that utilize GPU acceleration.

About memory expansion

This configuration is equipped with 32GB of memory, but depending on the application and situation, it may be effective to increase it to 64GB.
In the following cases, expansion can be expected to improve processing performance and stability.

・Insufficient memory in a 32GB environmentswapoccurs,Processing is slowCase
・Autodock Vina and GROMACSRunning multiple jobs simultaneouslyCase
- Calculation failed due to insufficient memoryIt is divided and executedCase

In these cases, increasing the memory to 64GB will improve processing speed and stability, and can be expected to be an effective solution to eliminate bottlenecks and bring out the full potential of the device.

However,Upgrading to 64GB doesn't necessarily solve the problem.
The amount of memory required for actual calculations varies greatly depending on the software used, data size, and number of parallel executions.
Before installing, we recommend checking your current usage and memory consumption.
If you have any questions or would like to discuss specific configurations, please feel free to contact Tegara.

For those who are active in these fields Drug Discovery Research Computational Chemistry Molecular biology Pharmacology Bioinformatics

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 Autodock Vina? AutoDock Vina is an open-source software specialized in molecular docking and virtual screening, and is widely used by drug discovery and structural biology researchers. In addition to its optimization algorithms that enable high-speed, high-precision calculations, it also features multi-threading support and simple operability. Because it is open source software, it can be used freely and without cost, and is increasingly being used in a variety of research settings, both in companies and universities. reference:GitHub – ccsb-scripps_AutoDock-Vina *Jumps to an external site What is vina-gpu? vina-gpu is a GPU-compatible version of Autodock Vina, which accelerates molecular docking using GPU parallel processing. It is up to 65 times faster than AutoDock Vina, enabling efficient large-scale virtual screening.It also provides a GUI that requires no installation, making it intuitive to use even without specialized knowledge. reference:GitHub "vina-gpu-2.0" *Jumps to an external site What is GROMACS? GROMACS is open source software that can perform molecular dynamics simulations on a scale of hundreds of thousands to millions of atoms at high speed. It supports advanced parallel calculations using GPUs and multi-core CPUs, allowing for efficient large-scale, long-term analysis. It also supports a variety of force fields, including AMBER and CHARMM, allowing for flexible handling of a wide range of molecular systems. reference:GROMACS Official Website *Jumps to an external site

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