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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 […]

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computing distributed computing GPUs molecular dynamics

GROMACS on AWS: compiling against CUDA

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 […]

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computing distributed computing molecular dynamics

GROMACS on AWS: compiling GCC

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 […]

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computing distributed computing GPUs molecular dynamics

GROMACS on AWS: Performance and Cost

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 […]

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computing distributed computing molecular dynamics

GROMACS on AWS

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 […]

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meetings molecular dynamics teaching

Analysing Simulation Data CECAM Workshop, Jülich, 14-15 October 2015

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 […]

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computing meetings molecular dynamics software carpentry teaching

CECAM Macromolecular simulation software workshop

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 […]

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computing GPUs molecular dynamics

Running GROMACS on an AMD GPU using OpenCL

I first used an Apple Mac when I was eight. Apart from a brief period in the 1990s when I had a PC laptop I’ve used them ever since. Until last year I had an old MacPro which had four PCI slots so you could add a GPU-capable NVIDIA card, although you were limited by […]

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molecular dynamics publication research

New Publication: Alchembed

In much of my research I’ve looked at how proteins embedded in cell membranes behave. An important part in any simulation of a membrane protein is, obviously, putting it into a model membrane, often a square patch of several hundred lipid molecules. This is surprisingly difficult: although a slew of methods have been published, none of […]

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molecular dynamics

Installing GROMACS with MPI support on a Mac

GROMACS is an optimised molecular dynamics code, primarily used for simulating the behaviour of proteins. To compile GROMACS you need, well, some compilers. I install gcc using MacPorts. Note that this requires you to first install Xcode. Then it is easy to install gcc version 4.9 by sudo port install gcc49 (and yes, I know […]