protoms ELBAlipids gcmc replica_exchange digital_filtering


  1. Computational Resources
  2. Software Resources
  3. Supplementary Information to Papers

Computational Resources


For production runs and serious simulations, the group is lucky to have access to Iridis 4. It consists of 12,320 processor-cores.

Recently, deployment of the fifth generation system, Iridis 5, has finished. This cluster is for dedicated use at the University of Southampton, and has been rated the most powerful academic supercomputer in the UK and as of 2017 one of the world’s top 500 supercomputers. It consists of more than 20,000 processor-cores.


ARCHER offers Supercomputing Service to the UK The Cray XC30 supercomputer contains 118,080 processing cores. Time is allocated by the HECBioSim or EPSRC/NERC consortia.


iSolutions is the University of Southampton's IT professional service. It provides and manages the IT equipment used within the group.

Software Resources


ProtoMS is a prototype protein Monte Carlo free energy simulation program developed by the group. This is used within the group to perform free energy calculations by FEP, FDTI, RETI and umbrella sampling featuring explicit or GBSA water models and the capability to work with hundreds of thousands of atoms.

The latest version of the code can be found by following the 'Download ProtoMS' link on the ProtoMS homepage.


Reversible Digitally Filtered Molecular Dynamics (RDFMD) is a method that selectively alters the vibrational motions within an MD simulation. It can be used to suppress or enhance the sampling in a molecular systems in a frequency-selective fashion.

The original paper for this enhanced sampling method can be found here.


The group have also developed code for indentification of novel protein binding sites by analysis of a MD trajectory by principal components analysis (PCA). This code is called 'PocketAnalyzer'; further information can be found in the following publication.

Supplementary Information to Papers

Supplementary information to papers can now be found on the Publications page.

School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ.