I have a github page which tracks some of the projects that I collaborate on. Probably it is more up to date than what you see here, but it does not correspond 1 to 1 in terms of the projects tracked.

If you use my code (or try and fail to use my code) then please send an email to the address on my page saying roughly what you used it for and how you got on. Its always interesting for me to hear from people solving actual problems with my work.

Discover amyloid aggregated structures for peptides

Ali Hakami-Zanjani's PhD work included development of some software to make accelerated simulations (accelerated relative to conventional replica exchange molecular dynamics) finding the aggregated configurations for systems of multiple amyloid peptides. He has archived this on his github page. The published simulations were for systems of 64 peptides treated atomistically with this code, then extended up to hundreds or thousands using coarse-graining methods. accelerated discovery of amyloid structures

Running with a system of a few dozen peptides, Ali's code accelerates aggregation, generating multiple (thermally disordered) quasi-equilibrium aggregated all-atom structures. Most of the structures found were anti-parallel beta sheet, for the systems considered (see picture, left, taken from Ali's thesis).

Rare Event Sampling with FRESHS

The FRESHS (Flexible Rare Event Sampling Harness System) code is online here. This is a parallel execution toolkit to combine the SPRES and FFS sampling algorithms with the LAMMPS, Gromacs and ESPResSo simulation programs (or with your own self-written code).

Full text of the paper which gives an in-depth look at the SPRES algorithm is behind a paywall at J Chem Phys, however you will find an earlier version of the paper on arXiv.

To cite the FRESHS software package refer to this paper: "The Flexible Rare Event Sampling Harness System (FRESHS)".

Free Energy Estimation Using AMBER

I have written a library implementing the techniques documented in this open access J Chem Theory Comput article as a plugin for AMBER. This is now available as part of the AmberTools14 release.

Cross Sectional Area

I recently embarked on a rewrite of the tumbling cross-section code which has garnered about 250 citations since I knocked it together as a PhD student with the help of sundry individuals from Alison Ashcroft's group. The idea is very simple, just sample over orientations of the molecule to estimate tumbling cross section, thence to find the friction with a buffer gas as it moves through the spectrometer. Sometimes simple things are also interesting and fun.


This is just a dump of files that I want to be available for whatever lab assignment or workshop. If you are just browsing then you probably won't have a use for any of this stuff: intro.pdf instructions.pdf