Living Journal of Computational Molecular Science: Announcements <p>The <a href="">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="">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: Promote your emerging software <p><span style="font-weight: 400;">Many of us not only use software, but develop tools as well, often with the broader community in mind. But how to get your work noticed and tried out by colleagues around the world? A user base is important to drive improvements, bug fixes, and impact.</span></p> <p><span style="font-weight: 400;">LiveCoMS wants to help! We plan to devote occasional blog posts (with social media advertising) to emerging software descriptions provided by developers. See guidelines below. These listings will create a marketplace for new tools that can serve developers and users.</span></p> <p><span style="font-weight: 400;">Guidelines for Software Listings</span></p> <ul> <li style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Your entire listing is limited to 1500 characters</span></li> <li style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">We may edit listings for length, format, and/or content (e.g., to improve clarity or avoid non-factual statements)</span></li> <li style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Your listing should explain where to obtain the software, the capabilities, and known limitations. Note who the developers are.</span></li> <li style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Note open-source status and availability to academics. Software not freely available to academics will not be listed at the present time.</span></li> <li style="font-weight: 400;" aria-level="1"><span style="font-weight: 400;">Indicate the best practices employed in code development/deployment:</span></li> <ul> <li style="font-weight: 400;" aria-level="2"><span style="font-weight: 400;">Github or similar code repository. </span></li> <li style="font-weight: 400;" aria-level="2"><span style="font-weight: 400;">Documentation type</span></li> <li style="font-weight: 400;" aria-level="2"><span style="font-weight: 400;">Availability of tutorials</span></li> <li style="font-weight: 400;" aria-level="2"><span style="font-weight: 400;">Degree of test coverage</span></li> <li style="font-weight: 400;" aria-level="2"><span style="font-weight: 400;">Is there a support/user group?</span></li> <li style="font-weight: 400;" aria-level="2"><span style="font-weight: 400;">Is the software containerized?</span></li> </ul> </ul> <p><span style="font-weight: 400;">If you have software you want to promote, send a listing addressing these issues to</span></p> Living Journal of Computational Molecular Science 2021-12-17 Blog Post: Editorial board opportunities at LiveCoMS <p><span style="font-weight: 400;">We are looking for additional people to contribute to this innovative, community-run journal beyond writing an article or acting as referee. As the journal expands coverage in additional areas of computation, including machine learning and quantum mechanical calculations, we need further expertise on our </span><a href=""><span style="font-weight: 400;">Editorial Board</span></a><span style="font-weight: 400;">. </span></p> <p><span style="font-weight: 400;">Is this for you? The time commitment is not very significant, but we can use the help of energetic creative researchers to help guide the journal as well as recruit and evaluate new articles. There is also a role to play as the journal’s Recording Secretary who, besides being an Editorial Board member, is a leadership role on the board that entails ensuring procedures are followed according to our </span><a href=""><span style="font-weight: 400;">by-laws</span></a><span style="font-weight: 400;">; the role require only a moderate time investment for an organized individual but represents a notable national service role. Applicants for the Editorial Board or Recording Secretary should have permanent positions (as faculty, in industry, at national labs, or equivalent) in fields relating to computational molecular science. We are also looking to expand the diversity of our Editorial Board both geographically and demographically.</span></p> <p><br /><span style="font-weight: 400;">If you’re interested in joining the Editorial board, or have any questions, please contact the managing editors at </span><a href=""><span style="font-weight: 400;"></span></a><span style="font-weight: 400;"> If you know of someone who may not not see this post or not on Twitter follow-ups, but appreciates what LiveCoMS is doing, please let them know about this opportunity!</span></p> Living Journal of Computational Molecular Science 2021-12-14 Blog Post: Issues logging in? Resolving one issue we have found <p>Update: It appears this problem has now been resolved.&nbsp; Please let us know ( if you consistently have problems logging in using Chrome with the error described below.&nbsp;</p> <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! <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=""><span style="font-weight: 400;"></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! <p>We are happy to announce <a href="">Volume 2, Issue 1 of LiveCoMS</a>! This issue includes the the first training article in our <a href="">newly expanded category</a> of “<a href="">Tutorials and Training Articles</a>”, giving careful and extensive advice on <a href="">how to compute interfacial properties</a>. It also includes a <a href="">massive compedium of experience and expertice on the topic of performing alchemical free energy calculations</a>, as well as <a href="">tutorials for GROMOS</a> and <a href="">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