antimicrobial resistance computing meetings molecular dynamics

BioExcel Alchemical Free Energy workshop

Last month I was invited to give a talk on using alchemical free energy methods to predict antimicrobial resistance at a workshop in Göttingen organised by the Max Planck Institute for Biophysical Chemistry on behalf of BioExcel. You can read more about the meeting, which I hope will become a biennial event, here.

antimicrobial resistance molecular dynamics publication research

New Publication: Predicting whether mutations confer resistance to an antibiotic

Due to the rise of antibiotic resistance, it is increasingly important that your clinician knows which antibiotics will work (and which will not). Traditionally, this is done in hospital microbiology labs by growing a sample taken from the infection site, and then testing how a range of antibiotics affect its growth, or, ideally, kill it. […]

distributed computing molecular dynamics

GROMACS in DOCKER: First Steps

DOCKER is cool. But what is it? From the DOCKER webpage Docker containers wrap up a piece of software in a complete filesystem that contains everything it needs to run: code, runtime, system tools, system libraries – anything you can install on a server. This guarantees that it will always run the same, regardless of […]

computing molecular dynamics skills

Setting up a GROMACS cluster

Recently I’ve moved to the John Radcliffe hospital and my old lab kindly let me have some old servers that were switched off. This pushed me to learn how to setup them up as a compute cluster with a scheduler for running GROMACS jobs. I’ve wanted to learn this for years, having used many clusters […]

computing molecular dynamics

How to setup a Gramble

This is a Gramble, which of course is short for a GROMACS Bramble, or, in other words, a Raspberry Pi 2 model B cluster running GROMACS. Given the ARM processor in a Raspberry Pi 2 does not allow SIMD instructions like the more complex (and expensive) Intel chips, why would I want to do such […]

computing molecular dynamics publication research

New Publication: Predicting affinities for peptide transporters

PepT1 is a nutrient transporter found in the cells that line your small intestine. It is not only responsible for the uptake of di- and tai-peptides, and therefore much of your dietary proteins, but also the uptake of most β-lactam antibiotics. This serendipity ensures that we can take (many of) these important drugs orally. Our […]