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...
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...
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...
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
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’re pleased to announce Sage 2.3.0 Release Candidate 2 (rc2)! Sage 2.3.0 will be the first OpenFF force field to use the AshGC neural network charge model, which was trained to AM1BCC ELF10 charges, and allows for rapid charge assignment for molecules with hundreds or thousands of heavy atoms.
📢 New software tutorial alert!
Gravelle et al introduce a suite of tutorials for new users of the LAMMPS simulation package, including molecular simulation basics, reactive force fields, GCMC and enhanced sampling #compchem
doi.org/10.33011/liv...
Interested in biomolecular simulation?
The latest article by Lier et al describes advanced tutorials for the GROMOS software, including free energy calculations, enhanced sampling and neural network potentials with SchNetPack! #compchem
livecomsjournal.org/index.php/li...
Table of contents figure
Our latest Best Practices article "Developing Monte Carlo Methodologies in Molecular Simulations" is out now and describes how to derive acceptance probabilities for a variety of Monte Carlo moves:
doi.org/10.33011/liv...
#compchem
Interesting history here that i was not really aware of. The same issues we’ve been dealing with in computational drug design for a while…
“Flexible schedule” in academia means you are free to work whenever you feel guilty.
My contacts here on know these topics already, but this could very well be a good intro for undergrads starting research, etc. I've previewed all the material, nice easy pace with good detail by a calm, welcoming instructor 2/2
@ckohlmeier.bsky.social here at CU Boulder just released a Coursera intro to Python for scientific computing. Different from other intro courses by emphasizing doing engineering calculations, like optimization and numerical integration. 1/2
Journalists keep asking me, baffled, “What’s the Trump administration really trying to do to the science agencies?”
So I say “They are trying to destroy them. Cut off their funding, ruin their facilities, harass their staff into leaving.”
It’s not reform, and it never was. It’s destruction.
“In nearly every industry, the United States’ most transformative innovations over the last eight decades depended on government funding, because the government was the most patient and reliable actor willing to take on risks for the public benefit.”
And China will reap the benefits.
Key thread here. NSF's own projections are that the success rate for competitive awards would drop from 26% to 7%, and the number of students, postdocs, and senior researchers involved in NSF research will drop by ~70% each, ~80% for undergrads. Perfect "Make China Great Again" policy.
NSF, NASA and NIH budgets per year, inflation adjusted from 2000-2025 along with the proposed cuts. NSF includes research component only. Massive cuts across all sectors, well below support spanning 25 years.
How bad will it be? Catastrophic.
Proposed cuts to #NSF, #NIH, and #NASA will set the US R&D landscape back 25 yrs+, cause economic and job loss now, and undermine innovations to come.
But, this is the WH's *proposed* budget.
Speak up now before it is too late.
(inflation adjusted $-s below)
This is the president's budget request to congress for 2026 for the National Science Foundation. Down 56%. Say goodbye to science as we know it in the US if this is remotely reflected in the final congressional bill. Most of the NSF funding ends up paying for PhD students in science.
The NSF's flagship fellowship program typically gives offers to 2,000+ young scientists. This year, in the face of looming budget cuts, that number was halved: only 1,000 received an offer. Our story on what that means for the science talent pipeline: www.nature.com/articles/d41...
unfortunate turn of events w total NSF #GRFP awards:
www.research.gov/grfp/Awardee...
year | awards offered:
2025 | 1000
2024 | 2036
2023 | 2555
2022 | 2193
...
2011 | 2077
there have been >2k awarded since 2010
(i intended to leave grad school if not for getting it in 2011)
damaging & dangerous!
We are pleased to announce a 2025 i-CoMSE virtual workshop on machine learning for molecules, coming up soon, April 28th-May 2nd, 2025! See www.i-comse.org/workshops for more info, and disseminate widely.
Direct registration link at: forms.gle/42Vzmw13F9Ht.... Register by Monday, April 21st!
If you, like me, do not particularly want to die by bleeding out of your eye sockets from diseases like Ebola, and think it's dumb to cut funding for viral countermeasures for future pandemics "because the COVID pandemic is over", here's something you can do about it:
resist.bot/petitions/PX...
LiveCoMS monthly PDF downloads from our current hosting site, where we moved in late 2021
Do LiveCoMS articles make a mark? Check out our new blog post on our download & viewing statistics. We’re excited to see LiveCoMS is having an impact and large numbers of people find our work valuable! livecomsjournal.org/index.php/li...
Artistic rendering of a biochemical model: a small molecule ligand, shown as a ball-and-stick model colored by element, is bound in a pocket in a protein surface, shown as a space filling model colored off-white.
We're changing the field of #compchem by creating free and open-source software for performing alchemical free energy calculations. Our flagship protocol calculates relative binding free energies of protein-ligand systems. Try it out in your browser: colab.research.google.com/github/OpenF...