Living Journal of Computational Molecular Science: Announcements https://www.livecomsjournal.org/index.php/livecoms <p>The <a href="http://livecomsjournal.org">Living Journal of Computational Molecular Science</a> (LiveCoMS) provides a peer-reviewed home for manuscripts which share best practices in molecular modeling and simulation. These works are living documents, <a href="https://livecomsjournal.github.io/about/paper_code/">regularly updated on GitHub with community input</a>, and can include perpetually updated reviews, tutorials, comparisons between software packages, and other documents which aim to improve the studies in the field and require ongoing updates.</p> en-US Fri, 23 Jul 2021 16:12:53 -0700 OJS 3.1.2.0 http://blogs.law.harvard.edu/tech/rss 60 Blog Post: LiveCoMS launches its new website! https://www.livecomsjournal.org/index.php/livecoms/announcement/view/35 <p><span style="font-weight: 400;">We are happy to announce the new, improved LiveCOMS website, for both published journal articles and new submissions.&nbsp; </span><span style="font-weight: 400;">Some nice features of the new site:</span></p> <ul> <li class="show" style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Perhaps most importantly, submissions will now have no article charges, making LiveCoMS a “diamond open access” journal, meaning it is completely </span><strong>free</strong><span style="font-weight: 400;"> for both authors and readers! (reminder, articles submitted without an approved presubmission letter will be rejected)&nbsp;</span></li> <li class="show" style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Direct links to the GitHub repositories and supporting information on individual article websites</span></li> <li class="show" style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Autogenerated citations</span></li> <li class="show" style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Better Google Scholar indexing</span></li> </ul> <p><span style="font-weight: 400;">There will likely be a few kinks to work through as we transition the websites, so if you see anything off, let us know at </span><a href="mailto:managing@livecomsjournal.org"><span style="font-weight: 400;">managing@livecomsjournal.org</span></a><span style="font-weight: 400;">.</span></p> <p><span style="font-weight: 400;">Many thanks to the University of Colorado Boulder for hosting the journal in its new configuration!</span></p> https://www.livecomsjournal.org/index.php/livecoms/announcement/view/35 Fri, 23 Jul 2021 16:12:53 -0700 Blog Post: LiveCoMS Volume 2, Issue 1 is complete! https://www.livecomsjournal.org/index.php/livecoms/announcement/view/15 <p>We are happy to announce <a href="https://www.livecomsjournal.org/issue/2658">Volume 2, Issue 1 of LiveCoMS</a>! This issue includes the the first training article in our <a href="https://www.livecomsjournal.org/post/888-tutorials-section-expands-to-tutorials-and-training-articles">newly expanded category</a> of “<a href="https://livecomsjournal.github.io/authors/tutorials/">Tutorials and Training Articles</a>”, giving careful and extensive advice on <a href="https://www.livecomsjournal.org/article/21385-a-guide-to-computing-interfacial-properties-of-fluids-from-molecular-simulations-article-v1-0">how to compute interfacial properties</a>. It also includes a <a href="https://www.livecomsjournal.org/article/18378-best-practices-for-alchemical-free-energy-calculations-article-v1-0">massive compedium of experience and expertice on the topic of performing alchemical free energy calculations</a>, as well as <a href="https://www.livecomsjournal.org/article/18552-a-suite-of-advanced-tutorials-for-the-gromos-biomolecular-simulation-software-article-v1-0">tutorials for GROMOS</a> and <a href="https://www.livecomsjournal.org/article/21383-aqua-duct-analysis-of-molecular-dynamics-simulations-of-macromolecules-with-the-use-of-molecular-probes-article-v1-0">AQUA-DUCT</a>.</p> <p>We hope the articles are of substantial use in your research, and please consider publishing your own lessons learned, software analyses, reviews, tutorials, and best practice documents in LiveCoMS!</p> https://www.livecomsjournal.org/index.php/livecoms/announcement/view/15 Fri, 19 Mar 2021 14:23:42 -0700 Blog Post: Tutorials section expands to Tutorials and Training Articles https://www.livecomsjournal.org/index.php/livecoms/announcement/view/33 <p>We are excited to announce the expanded scope of the (formerly) Tutorials category, which will now also encompass pedagogical articles about a particular computational technique or methodology that may, but need not be strictly tied to a particular piece of software. The category will be called <a href="https://livecomsjournal.github.io/authors/tutorials/">Tutorials and Training Articles</a>.</p> <p>We know that understanding the principles underpinning a given type of computation makes us better able to plan calculations, assess results and, of course, find bugs or glitches. However, even in our own pedagogically-oriented journal, there seemed no proper place for papers focused on more introductory aspects of computational molecular science not tied to a specific program. Voilà – an expanded category! Explicitly encouraging the publication of training articles is exactly consistent with our mission of improving the quality of computational molecular science and making it more accessible.</p> <p>What exactly should a training article look like? Well, you tell us. We will entertain any serious proposal that may be purely theoretical or more of a theory/tutorial hybrid. See details in the <a href="https://www.livecomsjournal.org/for-authors">For Authors</a> section. We hope that authors will come up with a range of great ways to teach important methodology to beginners and beyond.</p> https://www.livecomsjournal.org/index.php/livecoms/announcement/view/33 Mon, 01 Mar 2021 09:34:47 -0700 Blog Post: Second issue of LiveCoMS is out! https://www.livecomsjournal.org/index.php/livecoms/announcement/view/31 <p>We are happy to annouce the <a href="https://www.livecomsjournal.org/issue/1574">second issue of LiveCoMS</a>! This issue includes the very first articles in both of the categories of “Lessons Learned” (with articles on both <a href="https://www.livecomsjournal.org/article/9974-lessons-learned-in-atomistic-simulation-of-double-stranded-dna-solvation-and-salt-concerns-article-v1-0">simulation of DNA</a> and <a href="https://www.livecomsjournal.org/article/11073-lessons-learned-from-the-calculation-of-one-dimensional-potentials-of-mean-force-article-v1-0">calculation of potentials of mean force</a>) and “Software Analyses” (with an article on <a href="https://www.livecomsjournal.org/article/10409-raising-the-performance-of-the-tinker-hp-molecular-modeling-package-article-v1-0">ongoing speed improvements in the TINKER-HP package</a>), along with tutorial articles on the <a href="https://www.livecomsjournal.org/article/10607-a-suite-of-tutorials-for-the-westpa-rare-events-sampling-software-article-v1-0">WESTPA weighted ensemble package</a> and the <a href="https://www.livecomsjournal.org/article/10841-modeling-electrostatics-in-molecular-biology-a-tutorial-of-delphi-and-associated-resources-article-v1-0">DelPhi electrostatics package</a>.</p> <p>We hope the articles are of substantial use in your research, and please consider publishing your own lessons learned, software analyses, reviews, tutorials, and best practice documents in LiveCoMS!</p> https://www.livecomsjournal.org/index.php/livecoms/announcement/view/31 Mon, 02 Dec 2019 09:33:05 -0700 Blog Post: LiveCoMS “Software Analyses” papers https://www.livecomsjournal.org/index.php/livecoms/announcement/view/29 <p>Simulation software is of key importance for the computational molecular science community, as it is the basic “equipment” around which simulation research is structured. Modern simulation packages are numerous, get more and more complex every year, and require researchers to constantly gain new knowledge about the latest hardware platforms and programming.</p> <p>Sometimes, much of the useful information about simulation software that could benefit molecular simulation research is never published, or is published only in specialized books that are not easily accessible to the community. We need updated and openly accessible information about:</p> <ol> <li class="show">Comparisons of the reproducibility of a given property across different software package or hardware platforms;</li> <li class="show">HPC performance measures of a given simulation code on different platforms and architectures over time;</li> <li class="show">Ongoing development, advances, and improvements within a package directly impacting the users.</li> </ol> <p>To bring this information to the community, we have created a specific <a href="https://www.livecomsjournal.org/">LiveCoMS</a> category dedicated to <strong><a href="https://livecomsjournal.github.io/authors/software_analyses/">Software Analyses</a></strong> to allow the readers to keep up with technical developments and new possibilities of software. Such papers, like all other <a href="https://www.livecomsjournal.org/">LiveCoMS</a> papers, are peer-reviewed, and consist of a technical article describing in detail the code aspects and quantitative comparisons as the paper’s main focus. There is no limitation for the type of simulation software that can be included in such a paper; software packages of interest range from classical molecular dynamics and quantum chemistry to visualization and molecularly-oriented statistics and machine learning.</p> <p><strong><a href="https://livecomsjournal.github.io/authors/software_analyses/">Software Analyses</a></strong> should be updated to reflect updates or upgrades to the discussed package, as well as expanded for testing and comparison of new functionality. As with other <a href="https://www.livecomsjournal.org/">LiveCoMS</a> paper categories, authors can resubmit <strong><a href="https://livecomsjournal.github.io/authors/software_analyses/">Software Analyses</a></strong> for peer review again after significant updating, potentially resulting in a new publication and providing a way to get credit for this ongoing maintenance work and expansion. As with other <a href="https://www.livecomsjournal.org/">LiveCoMS</a> papers, authors are free to update their paper as often as they like; resubmission is required only when they want a new peer-reviewed version.</p> <p>We believe this new type of article will bring new possibilities to software developers to share their work and will be a important source of updated information for users.</p> <p>Jean-Philip Piquemal Lead Editor, Software Analyses section <a href="https://www.livecomsjournal.org/">Living Journal of Computational Molecular Science</a></p> https://www.livecomsjournal.org/index.php/livecoms/announcement/view/29 Fri, 19 Apr 2019 09:32:33 -0700