Resources

Hardware

  • Workstations: Many group members have a dedicated GPU workstation for their development work. We are based in room 234/234a in the Joseph Black Building, King’s buildings campus.
  • section6: The lab in-house GPU cluster (http://section6.chem.ed.ac.uk/ganglia/http://section6.chem.ed.ac.uk/ganglia/ only accessible from within the University subnet) hosts a mix of ca. 30 Tesla/GTX cards, and ca. 300 Intel Xeon/AMD Opteron processors. The cluster is located in the JCMB server room. Used to prototype simulations, perform trajectory analyses, and for GPU computing.
  • Eddie: The university of Edinburgh HPC cluster, (https://www.wiki.ed.ac.uk/pages/viewpage.action?spaceKey=ResearchServices&title=Eddie), hosts ca. 4000 cores and is used by group members for mid-size simulations.
  • ARCHER: Large scale molecular simulations are typically carried out on the UK’s national HPC (http://www.archer.ac.uk/http://www.archer.ac.uk/), the system hosts ca. 118,000 cores. 
Archer

Software

  • See the lab github page for a snapshot of the various ongoing software projects.
  • We are co-developers of the SireSire molecular simulation framework, and have developed an interface between the Sire and OpenMMOpenMM simulation libraries.  We also implement code in a number of other open-source software projects, for instance PLUMEDPLUMED
  • Group members use a variety of molecular simulation (e.g. GromacsGromacs, AMBER suiteAMBER suite and analysis (e.g. MDtrajMDtraj, PyEmmaPyEmma  packages depending on the needs of their project.
Open MM
Plumed

Wetware

  • We have several collaborations with other UoE groups that have expertise in related techniques (Alison Hulme  – Organic synthesis, Malcolm WalkinshawMalcolm Walkinshaw – crystallography and biophysics, Paul Barlow Paul Barlow – protein biochemistry, Dusan UhrinDusan Uhrin – NMR, Dave ClarkeDave Clarke – Mass spectrometry). We also collaborate with experimentalists elsewhere in the UK and beyond.
  • Protein expression and purification work is done in the Biological lab of the School of Chemistry, or at the Edinburgh Protein Production FacilityEdinburgh Protein Production Facility in the School of Biological Sciences. EPPF also provides access to well-maintained instruments for biophysical characterization (AutoITC200, BIAcore T200, SEC-MALS, DLS, CD, fluorescence spectrometers). The Edinburgh Biomolecular NMR unit maintains a range of high-field spectrometers (800 and 600-MHz Bruker Avance models).
  • Organic syntheses are carried out in Alison’s Hulme wet lab at the School of Chemistry.
Bionmr
EPPF
Alessio

Community

Julien is member of the management committee of the CCP-BioSimCCP-BioSim  and HEC-BioSimHEC-BioSim academic networks. Group members attend or deliver training workshops, and use or contribute software for the associated academic communities.

CCP Biosim
HEC BioSim
East Chem