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 workstation PC for AMBER MD.

Why choose us?

Parts like CPU cooler, Power Supply Unit, and chassis are often glossed over when putting together a system like this. Surprisingly, these parts have a massive effect on the lifespan and performance optimisation of the CPU, GPU and RAM. We only use parts that guarantee excellent cooling, airflow, and power delivery.

We’ve also got a lot of experience in putting these systems together, and our cable management is flawless. This not only means dust will be a lot less of an issue, but it will be much easier to work with when you eventually need an upgrade. This will only happen several years down the line, of course. Not to mention our cases just look fantastic.

Each Modena Computers Workstation is tailored to the personal needs of the user, but the features below would make for a great starting point for your AMBER computer.

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.

Speed might be another important factor for you depending on the other programs you might be using.

Most modern CPUs run at respectable frequencies, and AMD CPUs in particular have great IPC (Instructions per Clock).

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’s important to consider all of the programs that form your personal workflow, as these will dictate your overall system requirements. We’d love to give you a consultation and help you work all of this out. We have a lot of experience with a wide range of software, and a good understanding of which processes are handled by which components.


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

In fact, Nvidia is discontinuing their Quadro line of graphics cards, which makes it much easier for us to recommend sticking with a strong consumer grade card, such as one from Nvidia’s current RTX3000 series.

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.

These drives save a lot of time, and that means the PC will pay itself off a lot faster. You also still have the option of adding in some HDDs if you need to.


As we said before, each Modena Computers Vulcan 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.  

let's build the right computer for the job

Our consultants would be delighted to help you overcome your computing challenges and allow you to get on with your next 3D design, game, render, feature film, dieses curing machine learning simulation, architectural project or VR experience without your computers holding you back!

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