The idea for this paper arose during talking over coffee at the BioExcel Alchemical Free Energy workshop in May 2019. We’d previously shown that alchemical free energy methods could successfully predict which mutations in S. aureus DHFR confer resistance to trimethoprim (and crucially, which do not). That is all well and good, but to do […]
The story behind this preprint goes back to the workshop on free energy methods run by BioExcel in Göttingen in May 2019. I gave a talk, based in part on the work I’d previously published showing how alchemical free energy methods are able to predict which mutations in S. aureus DHFR confer resistance to trimethoprim.
HECBioSim advertised for proposals to use JADE, the new Tier-2 UK GPU high performance computer back in April 2019. JADE is built around NVIDIA DGX-1s, each of which contains 8 Tesla V100 GPUs. I’d previously run some alchemical free energy calculations on ARCHER, the Tier-1 UK academic supercomputer that has a conventional architecture, thanks to […]
It looks innocuous sitting on the desk, an Oxford Nanopore MinION, but it can produce a huge data of data from a single sequencing run. Since the nanowire works by inferring which base is in the pore by how much it reduces the flow of ions (and hence current) through the pore, the raw data […]
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 […]
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 […]