Our new shaker (New Brunswick 44R) arrived today. Tara seems pleased—certainly more so than the crew I assembled to move this beast.
New pipettes have arrived
The Gilson Fairy paid a visit to the lab today and left behind a wall of new pipettes.
Advances in Enhanced Sampling Workshop
This week I'm at the Advances in Enhanced Sampling Workshop in Telluride, CO. The workshop is focused on the latest advances in conformational sampling of biomolecular (and other) systems.
The program has a great line-up of speakers and topics. I'll be giving a talk later in the week on my work on optimizing replica exchange molecular dynamics (REMD) simulations.
Summer School Tutorials Starting
After two days of lectures from our great external speakers, we're now moving into three days of hands-on tutorials. We have three streams:
- Introduction to MD
- Introduction to Martini and coarse-graining
- QM/MM
Molecular Simulation Summer School Kickoff
The first day of the 2nd Annual Molecular Simulation Summer School is is kicking off today.
Moraine Lake in Banff National Park
We have approximately 30 students from around Canada, plus 30 local students from Calgary. We've brought in six external speakers, in addition to a few locals:
Qiang Cui (UW Madison) QM/MM Methods
Jeff Klauda (Maryland) Lipid simulations and force fields
Siewert-Jan Marrink (Groningen) Coarse grained models of membranes
Guillaum Lamoureux (Concordia) Polarizable force fields
José Faraldo-Gomez (NIH) Free energy landscapes and most probable paths
Justin MacCallum (Calgary) Combining simulation with experimental data
Wonpil-Im (Kansas) Modeling and simulation using CHARMM-GUI
Sergei Noskov (Calgary) Enhanced sampling of membrane transporters
Peter Tieleman (Calgary) Molecular simulations and Compute Canada
After two days of lectures, we then have 2.5 days of hands-on workshops, plus a trip to Banff.
Paper Accepted
Our paper "Single molecule conformational memory extraction: P5ab RNA hairpin" has been accepted for publication in the Journal of Physical Chemistry B.
Paper accepted
Our paper on "Extracting representative structures from protein
conformational ensembles" has been accepted for publication in Proteins: Structure, Function, and Bioinformatics.
Workshop on Free Energy Calculations in Drug Design
I just returned from the 2014 Workshop on Free Energy Calculations in Drug Design at Vertex Pharmaceuticals in Boston.
This meeting was interesting for me due to the number of attendees from industry---I would guess about half. I have not interacted with pharma much, so it was interesting to hear both "stories from the trenches" and thoughts about the role of free energy calculations in drug discovery.
While there was certainly plenty of skepticism about the role of free energy calculations in drug design, there was also guarded optimism. With the advent of GPU computing, these calculations are fast enough (or they will be soon) to provide answers on the timelines needed in industry. The usual question remain about force field accuracy and how to achieve sufficient sampling, but those will undoubtedly improve in the future.
Michael Shirts suggested that some of our most pressing problems are human in nature. How do we know that our codes are implemented correctly? Do we have enough testing? Are our software development practices solid enough? How do we ensure that practitioners are following best practices? What are best practices?
Overall, it was a great meeting. The next edition will be in 2016.
Website up and running
The new website is up and running, but we still need to flesh out the research section.