The use of advanced molecular simulation techniques often comes with additional computational and software requirements. Running molecular simulation and analysis tasks in the Cloud can significantly lower the barriers to use of advanced simulation methods and provides a cost-effective and practical solution for many molecular modeling tasks and for small and moderate size molecular dynamics simulations.

Cloud computing involves the use of computational equipment provided by a third-party, accessed through an internet connection, and paid for on an on-demand, as-needed basis. The cloud computing model provides researchers with access to powerful computational equipment that would otherwise be too costly to procure and maintain on their own. Tasks such as MDFF structure refinement often involve the use of multiple software suites, such as VMD for simulation preparation and Situs for initial rigid-body docking and VMD, NAMD, and ROSETTA for iterative refinement of models. Cloud platforms are also useful for bundling together all of the software packages used in a modeling workflow to gauruntee their availablity and interoperability on a standardized system.

We have adapted our molecular modeling applications NAMD, VMD, and associated tools to operate within the Amazon Web Servers (AWS) Elastic Compute Cloud (EC2) platform, enabling popular research workflows such as MDFF structure refinment and QwikMD simulation protocols to be run remotely by scientists all over the globe, with no need for investment in local computing resources and a reduced requirement for expertise in high performance computing technologies.

Using the molecular modeling virtual machine images

In order to access our EC2 virtual machine images, you will need to sign up for an AWS account. Be sure to read through Amazon's "Getting Started" Guide and the EC2 documentation before you begin. A PDF guide for accessing our EC2 image can be found here.

Choosing and launching a virtual machine instance

After reading through the Amazon documentation, you can launch one of our virtual machine images, either using the one-click launch in the Amazon Marketplace, or by selecting one of our production or test/development releases in the community AMI list when launching a new instance from the EC2 dashboard.

Hardware details for each EC2 instance type can be found here, and instance pricing is listed here.

Connecting to a newly-launched virtual machine instance

After launch, you can connect to your running instance through ssh, as described in the user's guide, with the user name 'ubuntu'. Alternatively, you can view the instance using a VNC client, such as NICE DCV Endstation. You can connect to the instance's public IP address on port 5901, using the first 8 characters of the instance id as the password. In order to connect to your instance through ssh and VNC, make sure you have the appropriate ports open in your Security Group:
22 tcp
5900-5920 tcp

One-click launch in the Amazon Marketplace

Our cloud virtual machine image is availble in the Amazon Marketplace, which allows users to use a very simple one-click launch using pre-configured choices of instance types that have been tested with our software.

Virtual machine images (Amazon AMIs)

In order to access our cloud virtual machine images, you will need to sign up for an AWS account. Be sure to read through Amazon's "Getting Started" Guide and the EC2 documentation.

After reading through the Amazon documentation, you can use any of our available cloud virtual machine images (AMIs) by searching for the listed AMI ID code on Amazon's publicly available AMI list when launching a new instance from the EC2 dashboard. See the EC2 documentation on finding shared AMIs using an AMI ID here.

Example of finding VMD/NAMD EC2 AMI image

    Production AMIs
  • (ami-a01125df) VMD-NAMD-VNC-R1.9.4.1, 64-bit Ubuntu Linux, EBS storage, HVM, created July 10, 2018
    Pre-release or developmental AMIs
  • (ami-0a7b3e90561695b4e) 64-bit Centos 7.5 Linux, EBS storage, HVM, created July 6, 2018
  • This is an experimental image using Centos and DCV for increased remote visualization performance and smoother interaction. This image has the DCV server already installed and running at launch and contains the latest build of VMD. To connect to this image requires using the DCV client software and connecting to the running instance on port 8443. The user name is "centos" and the password is "password". This image will only run on g3 instance types.

QwikMD Integrative Molecular Dynamics Toolkit for Novices and Experts

Guidance on running QwikMD on Amazon EC2.

Molecular Dynamics Flexible Fitting

Guidance on running MDFF structure refinment tasks on Amazon EC2.

NAMD Molecular Dynamics

Guidance on running NAMD molecular dynamics simulations on Amazon EC2.

VMD simulation preparation, analysis, and visualization

VMD can be used on Amazon EC2 both interactively and in batch mode for a variety of simulation preparation, visualization, and analysis tasks.

For trajectory or structure analysis work largely dominated by I/O, we recommend using instance types that support high performance networking such as "g3", "p3" (GPU-accelerated) or "m4", "c5", "r4" (CPU-only). In some cases, the use of instance-local SSDs for temporary storage may be beneficial for analysis tasks, and for those cases we would suggest using the "g2" (GPU-accelerated) instances.

For visualization work, we recommend running VMD on GPU-accelerated EC2 instance types such as g3s.xlarge, p3.2xlarge. The "g3" GPU-accelerated instances use Tesla M60 GPUs that perform well for general VMD visualization and analysis tasks. The "p3" GPU-accelerated instances use Tesla V100 GPUs, and are much more powerful and are better suited for large scale rendering and analytical workloads in VMD, due to their comparatively large 16GB on-board GPU RAM.

For parallel analysis or movie rendering workloads, the use of g3.16xlarge, p3.8xlarge, and p3.16xlarge instance types along with MPI-enabled VMD builds, but this is an expert-level feature that we don't currently provide a turnkey AMI for. If you're interested in running VMD in parallel on EC2, we are happy to provide guidance on this.