https://shabirahmad427.github.io/skaf-lab/software/SoftwaresHugo Blox Builder (https://hugoblox.com)en-usMon, 01 Jan 2024 00:00:00 +0000https://shabirahmad427.github.io/skaf-lab/media/icon_hu_16e4322de0c64ea4.pnghttps://shabirahmad427.github.io/skaf-lab/software/https://shabirahmad427.github.io/skaf-lab/software/cellulose-builder/Mon, 01 Jan 2024 00:00:00 +0000https://shabirahmad427.github.io/skaf-lab/software/cellulose-builder/<p><strong>Cellulose-Builder</strong> is a toolkit for generating crystalline cellulose structures ready for molecular dynamics simulations.</p> <h2 id="features">Features</h2> <ul> <li>Generates all major cellulose allomorphs (Iα, Iβ, II, III)</li> <li>Compatible with GROMACS, NAMD, AMBER</li> <li>Customizable microfibril dimensions</li> <li>Outputs standard PDB and topology files</li> </ul> <h2 id="citation">Citation</h2> <p>Gomes, T.C.F. &amp; Skaf, M.S. <em>Cellulose-Builder: A toolkit for building crystalline structures of cellulose</em>. <strong>Journal of Computational Chemistry</strong>, 2012. <a href="https://doi.org/10.1002/jcc.22959" target="_blank" rel="noopener">DOI: 10.1002/jcc.22959</a></p> <h2 id="download">Download</h2> <p>Available at: <a href="https://ftp.iqm.unicamp.br/pub/cellulose-builder" target="_blank" rel="noopener">ftp.iqm.unicamp.br/pub/cellulose-builder</a></p>https://shabirahmad427.github.io/skaf-lab/software/hpccs/Mon, 01 Jan 2024 00:00:00 +0000https://shabirahmad427.github.io/skaf-lab/software/hpccs/<p><strong>HPCCS</strong> (High Performance Collision Cross Section) is a fast and accurate software for calculating <strong>collision cross sections (CCS)</strong> of molecular ions, used in ion mobility spectrometry–mass spectrometry (IMS-MS) experiments.</p> <h2 id="features">Features</h2> <ul> <li>Based on the <strong>Trajectory Method (TM)</strong> — the gold standard for CCS calculation</li> <li>Parallelized with OpenMP for high performance</li> <li>User-friendly input/output</li> <li>Supports common molecular file formats</li> </ul> <h2 id="citation">Citation</h2> <p>Zanotto, L. et al. <em>High performance collision cross section calculation — HPCCS</em>. <strong>Journal of Computational Chemistry</strong>, 2018. <a href="https://doi.org/10.1002/jcc.25199" target="_blank" rel="noopener">DOI: 10.1002/jcc.25199</a></p> <h2 id="download">Download</h2> <div class="highlight"><pre tabindex="0" class="chroma"><code class="language-bash" data-lang="bash"><span class="line"><span class="cl">git clone https://github.com/cepid-cces/hpccs.git </span></span><span class="line"><span class="cl"><span class="nb">cd</span> hpccs </span></span><span class="line"><span class="cl">make </span></span></code></pre></div>