We wrote a response to a recent @science.org news article "NIH’s proposed caps on open-access publishing fees roil scientific community", in which we highlight the importance of community-run journals. Sadly our letter was rejected, but you can read it here:
livecomsjournal.org/index.php/li...
The first article of volume 7 is out now!
Learn how to simulate molecular dynamics in electronic excited states, beyond the Born-Oppenheimer approximation, with this best practices article by Prlj et al on nonadiabatic dynamics! #compchem
doi.org/10.33011/liv...
The latest article in our Lessons Learned category is out now!
"The Journey of Data: Lessons Learned in Modeling Kinase Affinity, Selectivity, and Resistance" by López-Ríos de Castro et al helps guide the development of platforms for structure-enabled ML for drug discovery: doi.org/10.33011/liv...
Funneling congressionally-mandated money away from universities to business. 20-30% cuts in NSF programs to fund X-labs.
New preprint describing our GNN charge model, AshGC!
Since QM methods of charge assignment scale poorly to larger molecules, and are also conformation dependent, AshGC leads to major performance improvements in this critical step in force field parameterization.
chemrxiv.org/engage/chemr...
Have you read about our GNN model for assigning partial charges? It's at the heart of both our Sage 2.3.0 force field and the protein force field we're developing. The paper was published last month in JCTC.
pubs.acs.org/doi/10.1021/...
In the latest @livecomsjournal.bsky.social
perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!:
livecomsjournal.org/index.php/li...
#compchem
Pretty much the death knell of US research universities as we know it. Industry scientists, if you want to have any graduate students applying to your posted jobs 5 years from now, have your bosses complain to congress/the administration. . .
'Alchemical' was not an allowed word in the NYT 'Spelling Bee' today.
If you're doing #alchemistry (alchemical free energy calculations) then here's release 2.5.0 of alchemlyb for you. github.com/alchemistry/...
(There's also the alchemlyb @joss-openjournals.bsky.social paper doi.org/10.21105/jos... if you want to read & cite.)
We report a new charge model and a new general small molecule force field. Here, we address the development and benchmarking of both the Open Force Field (OpenFF) AshGC charge model, as well as the Sa...
Partial atomic charges are a fundamental component underlying classical molecular simulations, but assigning charges remains a computational bottleneck; many common methods rely on quantum mechanical ...
New minor release of alchemlyb with fixes and enhancements. Supports Python 3.11 - 3.14. See CHANGES for details. What's Changed update action/checkout by @orbeckst in #417 Parallel read and prepro...
Been wondering why NSF isn't spending most of its FY26 appropriation? A $1.5B tech initiative may be the reason. And big cuts to hundreds of research programs could be just the beginning of the bad news. www.science.org/content/arti...
Oliver Beckstein [he/him]
Unexpected shift in funds has meant sharp drop in grants this fiscal year
And, here, in much more detail.
This is an absolutely critical read for all federally funded scientists and institutions.
Now is not the time to sit in the corner, hoping you won't be noticed - now is the time for action.
elizabethginexi.substack.com/p/summary-of...
