Puget Systems print logo
System Thumbnail

Recommended Systems for Molecular Dynamics


Recommended Workstations For




Single Xeon


Single Xeon E5 CPU

  • 1 GPU for GPU acceleration
  • Up to 128GB of RAM
  • Multiple SSD/HDD storage options

Dual Xeon


Dual Xeon E5 CPUs

  • 2 GPUs for GPU acceleration
  • Up to 512GB of RAM
  • Multiple SSD/HDD storage options

Which system is right for you?

There are so many different models, brands, and revisions of hardware that choosing the right components for your system can be a huge challenge. Dr. Kinghorn has taken the time to perform in-depth analysis on NAMD, GROMACS, and LAMMPS to determine what specifications impact molecular dynamics modeling and simulations the most. This ensures that you will be getting a system that has all the capabilities you need without spending money on components that will not be beneficial. For a great example of this, look at the video card section in the Hardware Recommendations.

While both of our recommended systems will give you incredible performance with molecular dynamics research, we have separated them based on a single and dual CPU configuration. This should allow you to get the best possible performance while staying within your budget. Luckily, these programs scale almost linearly so their is a direct correlation between the increase in cores and/or GPUs to the increase in performance that you will get in return.

Single Xeon Workstation

The Single Xeon Workstation utilizes Intel Xeon E5 V4 CPUs with GPU acceleration from a single GeForce GTX 1070 video card to achieve the performance of an 8-node CPU based cluster in a single, small form factor chassis.

This compact workstation is capable of up to 128GB of RAM and several hard drives to handle even moderate to large molecular dynamics simulations in a reasonable amount of time.

This system is built around our compact Peak Mini certified system, but with the non-relevant components removed. 

Dual Xeon Workstation

The Dual Xeon Workstation utilizes two Intel E5 V4 CPUs with GPU acceleration from two GeForce GTX 1070 or 1080 video cards to achieve the performance of a 16-node CPU based cluster in a single workstation.

It is capable of 512GB of RAM and 6+ hard drives to handle even your larger simulations. While this workstation will run you roughly twice the cost of the Single Xeon Workstation, the near linear scaling of NAMD, GROMACS, and LAMMPS allows for nearly twice the performance as well.

This system is built around our popular Peak Tower certified system, but with the non-relevant components removed.


Looking for more detail on our testing methods and why we chose this hardware for molecular dynamics programs? View our list of Recommended Hardware!

Why Choose Puget Systems?

Highly Reliable Product Line

All components in our product line are reviewed weekly. Any trends in failure rates are acted upon immediately, leaving us with a highly reliable product line that continues to improve. We do not add a part to our product line unless we feel we can stand behind it. This results in a high quality custom computer, that works as it should. You can feel confident that any selection you make on our website is a quality product.

Fast Build Times

By keeping inventory of our most popular parts, and maintaining a short supply line to parts we need, we are able to offer an industry leading ship time of 5-7 business days on nearly all our system orders.

We're Here, Give Us a Call!

We make sure our representatives are as accessible as possible, by phone and email. At Puget Systems, you can actually talk to a real person! We understand that personal service must be a priority for small businesses on the web. We are happy to provide as much help as you need, with no obligation to order. We understand that the best way to have satisfied customers is to help them make informed decisions before they buy!

Lifetime Support/Labor Warranty

When you buy a custom computer from Puget Systems, we are here to help you for life. Even when your parts warranty expires, we continue to answer your questions and even fix your computer with no labor costs.

Click here for even more reasons!