Highlights of our Work

Highlight: VMD and NAMD Soar to the Cloud

Molecule in the Cloud
Modern molecular simulation, visualization, and modeling techniques often require high-performance computing hardware to obtain the best efficiency. However, access to such hardware can be a barrier for some researchers. As an alternative, cloud computing provides a cost-effective and practical solution for many molecular modeling tasks and for small and moderate size molecular dynamics simulations. The cloud computing model provides researchers with access to powerful computational equipment that would otherwise be too costly to procure, maintain, and administer on their own. Additionally, cloud platforms can easily bundle different software packages used in a modeling workflow to guaruntee 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 Services (AWS) Elastic Compute Cloud (EC2) platform, enabling popular research workflows 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. Recent advancements in GPU virtualization technology now make it possible to use cloud computing for large-scale scientific computing, data analysis, and visualization tasks. The latest release of our cloud software can be run on EC2's latest graphics hardware, backed by DCV, to provide a smooth and seamless graphical working environment. Instance types specially designed for parallel CPU or GPU workloads provide users with access to the hardware they need to run even the most demanding features of NAMD and VMD, all from their much less powerful personal computers and even laptops. These instances can be paid for on an on-demand, as-needed basis, and some workflows, such as Molecular Dynamics Flexible Fitting, can be run for less than the cost of a cup of coffee. Our cloud virtual machine image is availble in the Amazon Marketplace, which provides users with a very simple one-click launch using pre-configured choices of instance types that have been tested with our software. To learn more, see our cloud research page.
Editorials

The Future of Biomolecular Modeling

A 2015 TCBG Symposium brought together scientists from across the Midwest to brainstorm about what's on the horizon for computational modeling. See a summary of what these experts foresee. Read more

Magnetic Sense of Birds

How do birds sense magnetic fields? Theoretical and computational biology may provide tools to unearth the answer. Researchers are combining behavioral studies with physics and chemistry to unlock the enigma of this sixth sense. By Lisa Pollack Read more

Remembering Klaus Schulten

Announcements

Sticky Business: tethering geometry and protein stabilitySimulation reveals how bacterial organelle converts sunlight to chemical energyNAMD used to predict behavior of Protein ComplexesGiuseppe Licari, honorable mention recipient of the Beckman Image Contest

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