Best Computer For AMBER MD

AMBER MD is used for molecular dynamics simulations. Most notably, this includes simulation of enzymes involved in biocatalysis, and drug interaction with protein receptors. An AMBER computer requires strong graphics processing power, but other parts in the system are necessary considerations to ensure that the GPUs are able to reach their full potential.

In this article, we’ll be talking about the components you need to build the Best Computer For AMBER MD.

CPU – Single-Thread or Multi-Thread?

Different software makes use of the CPU in different ways. To elaborate, certain software has tasks that use multiple cores, but other programs only really use 1 or 2 cores. 

Frequency is often conflated with this kind of performance, but this is not always the case. IPC (Instructions per Clock) is another important factor, and benchmark comparisons are more important than comparing GHz.

This makes it important to have the latest generation processor and platform in your system. Each new generation of processor will have increased single-threaded performance over the previous.

CPU multi-thread comparison
CPU single-thread comparison

The benchmarks above show how CPU performance can very between generations and platforms. 

A Threadripper is better for multi-threaded tasks, but is outperformed by a much more affordable Ryzen 7 in single-threaded processes. 

A previous generation i9 costs more than the Ryzen 7 and even has a higher boost frequency (5.0GHz vs 4.7GHz) but is outperformed in both areas.

CPU – Frequency

The CPU is not the main priority in an AMBER computer, but there are a few reasons that make it an important feature for AMBER.

Firstly, each model of CPU, along with the motherboard it’s installed in, supports a particular number of PCIe lanes. In this case, the lanes are used by the GPUs, with greater performance coming from more lanes.

Higher performance CPU/motherboard combinations have more lanes available, which means they’ll be able to better leverage the power of multiple graphics cards.

Keep in mind that the NVMe SSDs that we install in all of our PCs require 4 lanes, but these SSDs are necessary to maximise performance as well.

CPU – Core Count

With the relatively minimal CPU requirements of AMBER MD, an AMD Ryzen 5 5600X would be a great starting point, but other software such as TensorFlow can greatly benefit from higher core count CPUs.


It is common for PC builders and manufacturers to recommend Nvidia Quadro cards for these kinds of applications, but this is no longer necessary.

The RTX3060 is a great place to start, but an AMBER computer needs all the graphics power you can give it. While you shouldn’t skimp on the rest of your PC, especially if AMBER MD is not the only program you use, the graphics card should be your main priority when it comes to the allocation of your budget.

Our personal recommendation would be the Nvidia RTX3080, which has 10GB VRAM. 


There is no strict requirement for RAM in an AMBER computer, but as we move into the 2020s, 16GB should be considered the starting point.

Depending on the other software you use and the size of your projects, you might want to consider a bump up to 32GB, but beyond that, you probably wouldn’t make use of 64GB RAM.

Let us know what other programs you plan on using, and we’ll help you figure out your ideal RAM capacity.


Storage technology has come a long way over the past decade. Solid State Drives are known to be much faster than mechanical hard drives, but they’re also seen as pretty expensive.

It was pretty common to install the OS on a 120GB SSD, and everything else on a 1TB HDD, so that you could at least start up your PC super quickly.

Recently it’s become more viable to just use a larger SSD, from around 500GB to 1TB, and this is exactly our approach with our PCs. Having everything stored on SSDs means you’ll be able to save and load programs, and also transfer data, at incredible speeds. The SSDs we use are M.2 form factor and use the NVMe protocol, which means they take up no additional space in your case, and are even faster than standard 2.5” SATA drives.

Our Apollo systems currently feature PCIe 3.0 SSDs, and our Vulcan and Hydra system include even faster PCIe 4.0 SSDs.  


You also still have the option of adding in some HDDs if you need to store projects and media you are not actively working on. We would recommend adding these in at a later stage so you can prioritize parts like the CPU. 

Why choose us?

Often when you purchase a prebuilt system, it hasn’t even been switched on. If you’ve taken a look at our “Why Us?” page, you’ll already be aware of our unmatched assembly and testing processes, our swift and effective customer support, and our extensive technical knowledge and expertise.

Our team is comprised of lifelong computing enthusiasts with backgrounds in computer hardware and software, and we’re able to spot and resolve errors before the system is even shipped. By the time you receive your system, the likelihood of any kind of failure is as close to zero as possible. If you do encounter any issues, we’ll most likely be able to sort it out for you remotely, and in that rare case you’ll need to send the system in, you’ll be covered by our 3-Year (or 4-Year) warranty and lifetime hardware support.

Our systems combine the performance of enthusiast grade components and the stability of professional workstations. Yes, there are other places you can spend your money, but in terms of actual performance and quality, we simply have no competition. 


As we said before, each Modena Computers Workstation is custom built to the workflow and budget requirements of its user. It’s important to consider other programs you may want to use with this workstation.

During our consultation process, you can let us know exactly which programs you want to use with your machine, and we’ll be happy to help you understand what you need. 

Keep in mind that opting for higher performance right out of the gate offers much greater value than getting exactly what you need right now. A higher performance PC won’t need downtime to upgrade any time soon, and will also allow you to complete more work in less time. It could pay itself off a lot sooner than a more affordable option.  

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