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#forcefield

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Piia Bartos<p>We recently published a study where we compared a few common force fields and their usability with RNA-protein complexes.</p><p>Shortly: All the force fields (ff14SB/ff19SB+OL3, OPLS4, AMOEBA) produce okay simulations. Polarization (AMOEBA force field or O3P water) might cause structural instability if protein has longer loops. </p><p><a href="https://mstdn.science/tags/compchem" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>compchem</span></a> <a href="https://mstdn.science/tags/RNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>RNA</span></a> <a href="https://mstdn.science/tags/protein" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>protein</span></a> <a href="https://mstdn.science/tags/forcefield" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>forcefield</span></a> <a href="https://mstdn.science/tags/simulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>simulation</span></a> <a href="https://mstdn.science/tags/publication" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>publication</span></a> </p><p><a href="https://www.frontiersin.org/articles/10.3389/fchem.2023.1217506/full" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://www.</span><span class="ellipsis">frontiersin.org/articles/10.33</span><span class="invisible">89/fchem.2023.1217506/full</span></a></p>
@Om<p>squirrel encounters force field...</p><p><a href="https://mastodon.social/tags/squirrel" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>squirrel</span></a> <a href="https://mastodon.social/tags/glass" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>glass</span></a> <a href="https://mastodon.social/tags/door" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>door</span></a> <a href="https://mastodon.social/tags/encounters" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>encounters</span></a> <a href="https://mastodon.social/tags/forcefield" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>forcefield</span></a> <a href="https://mastodon.social/tags/gaveup" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>gaveup</span></a> <a href="https://mastodon.social/tags/animatedgif" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>animatedgif</span></a></p>
@Om*<p>squirrel encounters force field...</p><p><a href="https://mastodon.cloud/tags/squirrel" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>squirrel</span></a> <a href="https://mastodon.cloud/tags/glass" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>glass</span></a> <a href="https://mastodon.cloud/tags/door" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>door</span></a> <a href="https://mastodon.cloud/tags/encounters" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>encounters</span></a> <a href="https://mastodon.cloud/tags/forcefield" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>forcefield</span></a> <a href="https://mastodon.cloud/tags/gaveup" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>gaveup</span></a> <a href="https://mastodon.cloud/tags/animatedgif" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>animatedgif</span></a></p>
Martin Vögele<p>New <a href="https://fediscience.org/tags/preprint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>preprint</span></a> about PENSA, our flexible <a href="https://fediscience.org/tags/OpenSource" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>OpenSource</span></a> software package for comprehensive and thorough investigation of biomolecular conformational ensembles:</p><p><a href="https://arxiv.org/abs/2212.02714" rel="nofollow noopener noreferrer" target="_blank"><span class="invisible">https://</span><span class="">arxiv.org/abs/2212.02714</span><span class="invisible"></span></a></p><p>In three real-world examples, we show how it can be used to understand an <a href="https://fediscience.org/tags/enzyme" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>enzyme</span></a> mechanism, <a href="https://fediscience.org/tags/DNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>DNA</span></a> <a href="https://fediscience.org/tags/forcefield" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>forcefield</span></a> parameters, and <a href="https://fediscience.org/tags/signaling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>signaling</span></a> in an <a href="https://fediscience.org/tags/opioid" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>opioid</span></a> <a href="https://fediscience.org/tags/receptor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>receptor</span></a>.</p><p>Please share widely with the <a href="https://fediscience.org/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MolecularDynamics</span></a> <a href="https://fediscience.org/tags/simulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>simulation</span></a> <a href="https://fediscience.org/tags/CompChem" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>CompChem</span></a> <a href="https://fediscience.org/tags/MolBio" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>MolBio</span></a> <a href="https://fediscience.org/tags/StructuralBiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>StructuralBiology</span></a> <a href="https://fediscience.org/tags/GPCR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#<span>GPCR</span></a> communities!<br>Feedback and ideas are always welcome.</p>
TJ<p>Somewhat disappointed to learn that <a href="https://mastodon.bida.im/tags/forcefield" class="mention hashtag" rel="tag">#<span>forcefield</span></a> technology remains basically in the early theoretical stages.</p>
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