Michael Shirts
@michaelshirts.bsky.social
Professor, University of Colorado Boulder, molecular modeling and computational infrastructure
Reposted by Michael Shirts
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
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
October 28, 2025 at 3:36 PM
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
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
Reposted by Michael Shirts
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.)
(There's also the alchemlyb @joss-openjournals.bsky.social paper doi.org/10.21105/jos... if you want to read & cite.)
2.5.0 · alchemistry alchemlyb · Discussion #445
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...
github.com
October 23, 2025 at 5:17 PM
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.)
(There's also the alchemlyb @joss-openjournals.bsky.social paper doi.org/10.21105/jos... if you want to read & cite.)
Reposted by Michael Shirts
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.
October 10, 2025 at 3:02 PM
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.
Reposted by Michael Shirts
📢 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...
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...
October 2, 2025 at 2:35 PM
📢 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...
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...
Reposted by Michael Shirts
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...
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...
September 30, 2025 at 5:06 PM
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...
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...
Reposted by Michael Shirts
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
doi.org/10.33011/liv...
#compchem
August 11, 2025 at 6:32 PM
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
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…
Just posted a 2nd comment regarding this meeting, based on an experience that I had at NIGMS.
We heard from leaders of computational chemistry sections at leading computational chemistry divisions within pharmaceutical companies that they were frustrated by the quality of the extant methods.
1/n
We heard from leaders of computational chemistry sections at leading computational chemistry divisions within pharmaceutical companies that they were frustrated by the quality of the extant methods.
1/n
July 13, 2025 at 5:47 PM
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…
Reposted by Michael Shirts
“Flexible schedule” in academia means you are free to work whenever you feel guilty.
July 11, 2025 at 8:26 PM
“Flexible schedule” in academia means you are free to work whenever you feel guilty.
@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
Introduction to Python for Scientific Computing
Offered by University of Colorado Boulder. Whether you’re a scientist, engineer, student, or industry professional working with data or ... Enroll for free.
www.coursera.org
July 3, 2025 at 5:59 PM
@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
Reposted by Michael Shirts
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.
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.
NEW: NSF will be kicked out of their building. Announcement will be made tomorrow by HUD Sec. and Governor of VA. HUD will take over the NSF building over the next two years.
NSF staffer: "There is no planning for NSF, no identified future location, appropriation for a new building or a move."
NSF staffer: "There is no planning for NSF, no identified future location, appropriation for a new building or a move."
June 24, 2025 at 10:34 PM
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.
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.
Reposted by Michael Shirts
Reposted by Michael Shirts
“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.
And China will reap the benefits.
Trump Is Killing American Innovation
China will reap the benefits.
www.foreignaffairs.com
May 31, 2025 at 3:37 PM
“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.
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.
I am looking at NSF's budget request, in awe at the disinvestment in learning anything. nsf-gov-resources.nsf.gov/files/00-NSF...
nsf-gov-resources.nsf.gov
May 31, 2025 at 9:32 AM
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.
Reposted by Michael Shirts
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)
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)
May 31, 2025 at 2:50 AM
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.
Presidential budget is out. Here's NSF. Biggest cut, by amount, is $1 billion, or 66.8%, from MPS (Physics & Math directorate). nsf-gov-resources.nsf.gov/files/00-NSF...
May 31, 2025 at 12:11 AM
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.
Reposted by Michael Shirts
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...
NSF slashes prestigious PhD fellowship awards by half
US National Science Foundation announces lowest number of Graduate Research Fellowship Programme recipients in 15 years.
www.nature.com
April 8, 2025 at 10:15 PM
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...
Reposted by Michael Shirts
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!
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!
Research.gov :: GRFP
www.research.gov
April 8, 2025 at 12:53 PM
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!
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!
Direct registration link at: forms.gle/42Vzmw13F9Ht.... Register by Monday, April 21st!
Workshops
www.i-comse.org
April 4, 2025 at 3:11 PM
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!
Direct registration link at: forms.gle/42Vzmw13F9Ht.... Register by Monday, April 21st!
Reposted by Michael Shirts
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...
resist.bot/petitions/PX...
Reinstate funding for pandemic prevention research and preparedness
Text SIGN PXNIDH to 50409 to send this to your officials.
resist.bot
March 28, 2025 at 12:48 AM
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...
resist.bot/petitions/PX...
Reposted by Michael Shirts
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...
March 25, 2025 at 9:32 PM
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...
Reposted by Michael Shirts
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...
February 4, 2025 at 2:46 PM
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...