livecomsjournal
The Living Journal of Computational Molecular Science (LiveCoMS) provides a peer-reviewed home for computational molecular science papers that can and should be updated. livecomsjournal.org
- 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...
- And feel free to make suggestions on the article at the authors' Github repository: github.com/ispg-group/b...
- Interested in simulating modified nucleic acids? The latest tutorial article by Galindo-Murillo et al details the steps needed to parameterize and run the simulations in the AMBER ecosystem with modXNA! #compchem doi.org/10.33011/liv...
- As ever you are encouraged to make suggestions at the authors' Github repo: github.com/ManghraniA/M...
- 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...
- As ever, you can comment on and contribute to the paper at the authors' GitHub repo: github.com/openkinome/k...
- Reposted by livecomsjournalChapin Cavendar's paper, Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields, is out now in LiveCoMS. Read it for a detailed look at the great work he has been doing toward an OpenFF protein force field, and stay tuned! livecomsjournal.org/index.php/li...
- 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
- Be sure to comment on the paper at the authors' Github repo: github.com/openforcefie...
- "Scientists are well aware that they seem to be getting a bad deal." www.theguardian.com/science/2017... 8 years ago, in response to this article, we wrote about the need for LiveCoMS, a diamond open access journal with no charge for submissions or for libraries: livecomsjournal.org/index.php/li...
- Since then, we've published six volumes of peer-reviewed living documents, covering perpetually updated reviews, tutorials & software comparisons. Every article has its own GitHub repo for community discussion, and we're starting to publish 2nd versions with important scientific updates.
- Here's why we think this is still important today: livecomsjournal.org/index.php/li... But we'd love to continue that debate! What do you like about LiveCoMS, what made you publish with us or read an article? Or what can we do better, what is holding you off submitting your first manuscript?
- 📢 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...
- You can find accompanying files and comment on the article here: github.com/lammpstutori...
- 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...
- This is version 2 of this tutorial article, illustrating our 'living document' approach to publishing in which works are regularly updated on Github with community input. As ever, you can comment on this article here: github.com/biomos/gromo...
- The latest @livecomsjournal.bsky.social tutorial "Molecular Dynamics: From Basics to Application" by Vollmers, Chen et al is out now! doi.org/10.33011/liv... It includes comprehensive MD tutorials in GROMACS, covering forcefields, thermodynamic ensembles, long-range electrostatics and much more!
- As ever you can comment on and contribute to the work via the accompanying GitHub repo: github.com/Foly93/MD_Fr...
- Interested in solvation free energies of small molecules and proteins? The latest @livecomsjournal.bsky.social tutorial by Egger-Hoerschinger et al provides a guide to quantifying hydration thermodynamics using Grid Inhomogeneous Solvation Theory (GIST): doi.org/10.33011/liv... #compchem
- Accompanying code is available at: github.com/liedllab/gis...
- 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
- You can comment on the manuscript and find code examples at the accompanying github repo: github.com/usnistgov/be...
- Interested in enhanced sampling for molecular dynamics simulations? Check out the latest LiveCoMS tutorial on Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD: livecomsjournal.org/index.php/li... #compchem
- As always, if you have any comments or questions on the paper, you're encouraged to engage with the paper's Github repository: github.com/Lemkul-Lab/g...
- Reposted by livecomsjournalHappy to announce our latest article, a tutorial on running Gaussian-accelerated MD simulations in NAMD. Tour de force work by @hmmichel.bsky.social with @mdpoleto.bsky.social that unifies theory and practice in one place! livecomsjournal.org/index.php/li...
- Reposted by livecomsjournalIn the London heat, dreaming of a chemistry journal where articles evolve (living, versionable, open). Has anyone tried F1000? I am curious what the experience is like #OpenScience #ChemSky
