Living Journal of Computational Molecular Science: Announcements https://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 Blog Post: Issues logging in? Resolving one issue we have found https://livecomsjournal.org/index.php/livecoms/announcement/view/39 <p>Most users should not need to register to the web site - only authors and reviewers. &nbsp;However, those people DO need to log in and some people are having issues with the login process. The symptom is that after clicking "Login", the login fails and then the "Username" and "Password" fields are blanked out. This is different than if the password or username is wrong, which which case an error message will be displayed.&nbsp;</p> <p>This is a known issue, and we are still working on a resolution (the IT people are having a hard time reproducing it . . . ). It appears that some people have a hard time logging in with Chrome - it varies from person to person, but is mostly consistent per Chrome installation (i.e. there are no consistent ways to fix it if it is failing.&nbsp; Right now, the only fix is to use a different browser. Safari seems to work relatively consistently, as does Microsoft Edge. &nbsp;We'll keep working on addressing this!</p> Living Journal of Computational Molecular Science 2021-11-17 Blog Post: LiveCoMS launches its new website! https://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> Living Journal of Computational Molecular Science 2021-07-23 Blog Post: LiveCoMS Volume 2, Issue 1 is complete! https://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> Living Journal of Computational Molecular Science 2021-03-19 Blog Post: Tutorials section expands to Tutorials and Training Articles https://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> Living Journal of Computational Molecular Science 2021-03-01 Blog Post: Second issue of LiveCoMS is out! https://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> Living Journal of Computational Molecular Science 2019-12-02