If you want to compile GROMACS to run on a GPU Amazon Web Services EC2 instance, please first read these instructions on how to compile GROMACS on an AMI without CUDA. These instructions then explain how to install the CUDA toolkit and compile GROMACS against it. The first few steps are loosely based on these […]
These are some quick instructions on how to build a more recent version of GCC than is provided by the devel-tools package on the Cent OS based Amazon Linux AMI. (currently GCC 4.8.3) You may, for example, wish to use a more recent version to compile GROMACS – that is my interest. If so, then […]
So we have created an Amazon Machine Image (AMI) with GROMACS installed. In this post I will examine the sort of single core performance you can expect and much this is likely to cost compared to other compute options you might have. Benchmark To test the different types of instances you can deploy our GROMACS […]
In this post I’m going to show how I created an Amazon Machine Instance with GROMACS 5.0.7 installed for use in the Amazon Web Services cloud. I’m going to assume that you have signed up for Amazon Web Services (AWS), created an Identity and Access Management (IAM) user (each AWS account can have multiple IAM […]
This two day workshop on Analysing Simulation Data was part of the larger CECAM Macromolecular Simulation Software Workshop at the Forschnungzentrum, Jülich that I co-organised. It was the second workshop and immediately followed an introductory Software Carpentry workshop. Prior to a few years ago I analysed all my simulation data using either VMD, often by […]
I’m co-organiser of this slightly-different CECAM workshop in October 2015 at the Forschungszentrum Jülich, Germany. Rather than following the traditional format of 3-4 day populated by talks with the odd poster session, this is an extended workshop made up of six mini-workshops. Since it is focussed on python-based tools for biomolecular simulations, of which there are an increasing number, the […]