GitHub - ispg-group/best-practices-namd: Best practices Guide on nonadiabatic molecular dynamics Best practices Guide on nonadiabatic molecular dynamics - ispg-group/best-practices-namd

And feel free to make suggestions on the article at the authors' Github repository: github.com/ispg-group/b...

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...

As ever you are encouraged to make suggestions at the authors' Github repo: github.com/ManghraniA/M...

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 can comment on and contribute to the paper at the authors' GitHub repo: github.com/openkinome/k...

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...

Chapin 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...

GitHub - openforcefield/review-protein-benchmark-datasets Contribute to openforcefield/review-protein-benchmark-datasets development by creating an account on GitHub.

Be sure to comment on the paper at the authors' Github repo: github.com/openforcefie...

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

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?

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.

Is the staggeringly profitable business of scientific publishing bad for science? The long read: It is an industry like no other, with profit margins to rival Google – and it was created by one of Britain’s most notorious tycoons: Robert Maxwell

"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...

GitHub - lammpstutorials/lammpstutorials-article: A Set of Tutorials for the LAMMPS Simulation Package A Set of Tutorials for the LAMMPS Simulation Package - lammpstutorials/lammpstutorials-article

You can find accompanying files and comment on the article here: github.com/lammpstutori...

📢 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...

Hi, we have a few relevant tutorials out recently including MD with e.g. gromacs, gromos and biosimspace: livecomsjournal.org/index.php/li...

GitHub - biomos/gromos_tutorial_livecoms: Advanced tutorial for the GROMOS software for biomolecular simulation Advanced tutorial for the GROMOS software for biomolecular simulation - biomos/gromos_tutorial_livecoms

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...

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...

GitHub - Foly93/MD_FromBasicsToApplication: Elaborate Tutorial for Teaching Molecular Dynamics directed to university students in their graduate program. The course is designed to be finished within one semester, but can be completed within a couple of weeks technically speaking. Elaborate Tutorial for Teaching Molecular Dynamics directed to university students in their graduate program. The course is designed to be finished within one semester, but can be completed within ...

As ever you can comment on and contribute to the work via the accompanying GitHub repo: github.com/Foly93/MD_Fr...

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!

GitHub - liedllab/gist-tutorial: GIST Tutorial published in the Living Journal of Computational Molecular Science GIST Tutorial published in the Living Journal of Computational Molecular Science - liedllab/gist-tutorial

Accompanying code is available at: github.com/liedllab/gis...

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

GitHub - usnistgov/best-practices-mc Contribute to usnistgov/best-practices-mc development by creating an account on GitHub.

You can comment on the manuscript and find code examples at the accompanying github repo: github.com/usnistgov/be...

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

GitHub - Lemkul-Lab/gamd_livecoms_tutorial Contribute to Lemkul-Lab/gamd_livecoms_tutorial development by creating an account on GitHub.

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...

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

Happy 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...

In 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

That's right - all articles are diamond open access and can be regularly updated!

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...

The Living Journal of Computational Molecular Science (LiveCoMS) is on BlueSky! Check out our recent blog post on why @livecomsjournal.bsky.social matters to find out more about us: livecomsjournal.org/index.php/li... #compchem #chemsky