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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<link rel="stylesheet" href="./css/style.css" />
<link rel="apple-touch-icon" sizes="180x180" href="/apple-touch-icon.png" />
<link rel="icon" type="image/png" sizes="32x32" href="/favicon-32x32.png" />
<link rel="icon" type="image/png" sizes="16x16" href="/favicon-16x16.png" />
<link rel="manifest" href="/site.webmanifest" />
<script
src="https://kit.fontawesome.com/7a6b0f1824.js"
crossorigin="anonymous"
></script>
<title>SENPAI</title>
</head>
<body>
<header>
<h1>SENPAI Molecular Dynamics</h1>
<h3>-- Cheminformatics for the 21st Century --</h3>
</header>
<div class="links">
<i class="fa-brands fa-github"></i>
<a
href="https://github.com/SENPAI-Molecular-Dynamics/SENPAI"
>
GitHub Repository
</a>
<i class="fa-solid fa-envelope"></i>
<a href="mailto:chelsea486mhz@protonmail.com">Email</a>
</div>
<main>
<div>
<h2>What is SENPAI?</h2>
<figure style="float: right; width: 40%">
<img src="./img/senpai.png" alt="" style="width: 100%" />
<figcaption style="text-align: center">
SENPAI being used to simulate a deep eutectic solvent
</figcaption>
</figure>
<p>
SENPAI (Simplified Evolutive N-body Processing And Integration) is a
free, open source molecular dynamics simulator licensed under the
GPLv3.
</p>
<p>
Given 3D representations of chemical substrates (to the atomic level),
and a user-selected mathematical model of the universe, SENPAI will
simulate the motion within 3D space of the provided substrates and
provide the user with a plethora of information regarding the state of
each atom during the simulation.
</p>
<p>
SENPAI provides many tunable parameters, and allows for flawless
script integration to better incorporate SENPAI in your workflow.
</p>
</div>
<div>
<h2>Noteworthy Features</h2>
<ul>
<li>
<strong>Integrated potential reduction:</strong> Easily mitigate the
issue of "garbage in, garbage out"! If told to do so, SENPAI will
reduce the potential energy of the system to a user-selected target
value before simulating. SENPAI sequentially runs several algorithms
like gradient descent to properly set the system up for simulation.
</li>
<li>
<strong>Analytical differentiation:</strong> Traditional MD
simulators compute a particle's total potential and numerically
differentiate it to compute the applied force. SENPAI analytically
solves for the force vector, resulting in an extreme speedup. Should
you prefer numerical potential differentiation, SENPAI offers two
different numerical differentiation methods which can be configured
as well!
</li>
<li>
<strong>Easy to use file formats:</strong> The MDS, MDM, and MDP
file formats developped for SENPAI can be hand-written! No need for
special software. Quickly and easily prepare simulations and adjust
them with no hassle. Simulations are rendered as XYZ, and can be
immediately viewed using existing software without prior conversion!
</li>
<li>
<strong>Efficient computing model:</strong> the ONICHaN (Optimized
Numerical Integration, Classical Harmonics, and N-body) model was
tailored for SENPAI over months of work. Inspired by the AMBER
family of force fields, it allows SENPAI to compute forces with
unprecedented efficiency.
</li>
</ul>
</div>
<div class="grid">
<div class="grid_item">
<h2>Source code</h2>
<p>Download the senpai source code here:</p>
<ul>
<li>
<a
href="https://gitlab.chelsea486mhz.fr/Chelsea486MHz/senpai/-/releases"
>Personal GitLab</a
>
</li>
<li>
<a href="https://github.com/Chelsea486MHz/senpai/releases/"
>GitHub</a
>
</li>
<li>
<a href="./src/senpai-1.1-1.tar.gz">Latest release (1.1)</a>
</li>
<li>
<a href="./src/senpai-1.1-1.tar.gz">Release 1.1-1 (24-04-2022)</a>
</li>
<li>
<a href="./src/senpai-1.0.tar.gz">Release 1.0 (18-01-2022)</a>
</li>
</ul>
</div>
<div class="grid_item">
<h2>User manuals</h2>
<p>Some manuals to get you started with SENPAI</p>
<ul>
<li>
<a href="./manuals/installation/">Installing SENPAI</a>
</li>
<li>
<a href="./manuals/first-simulation/">Your first simulation</a>
</li>
<li>
<a href="./manuals/mds-format/"
>Creating substrates (MDS files)</a
>
</li>
<li>
<a href="./manuals/mdm-format/">Creating models (MDM files)</a>
</li>
</ul>
</div>
<div class="grid_item">
<h2>Technological Demonstrations</h2>
<p>
The following simulations are available as technological
demonstrations. A working SENPAI 1.0+ installation is required to
run them.
</p>
<ul>
<li>
<a href="./simulations/16-water.tar.gz"
>16 water molecules at STP</a
>
</li>
<li>
<a href="./simulations/64-water.tar.gz"
>64 water molecules at STP</a
>
</li>
</ul>
</div>
</div>
<div class="grid_item">
<h2>Installation (RPM)</h2>
<p>
SENPAI MD provides an RPM repository for RHEL-based distributions of Linux. Officially, SENPAI is only tested on Almalinux 8.5, but it should work on anything RPM-based.
</p>
<ul>
<li>
<p>Install the SENPAIMD repo: # curl https://senpaimd.org/repo/rpm/x86_64/repodata/senpaimd.repo > /etc/yum.repos.d/senpaimd.repo</p>
</li>
<li>
<p>Install its PGP key: # curl -O https://senpaimd.org/repo/rpm/RPM-GPG-KEY-senpaimd && rpm --import RPM-GPG-KEY-senpaimd</p>
</li>
<li>
<p>Refresh your repo cache and install the package: # dnf update && dnf install senpai</p>
</li>
</ul>
</div>
<div class="grid_item">
<h2>Installation (ISO) (BETA!)</h2>
<p>
SENPAI MD provides an ISO image that deploys an AlmaLinux 8.5 system with a SENPAI worker pre-installed. This installer is a work in progress and is NOT YET READY FOR PRODUCTION USE.
</p>
<ul>
<li>
<p>Download the ISO here: <a href="./iso/SENPAI-8.5-1-x86_64.iso">SENPAI-8.5-1.x86_64.iso</a></p>
</li>
<li>
<p>Download its SHA256 checksum here: <a href="./iso/SENPAI-8.5-1-x86_64.iso.sha256sum">SENPAI-8.5-1.x86_64.iso.sha256sum</a></p>
</li>
</ul>
</div>
</div>
<div class="grid_text">
<h2>Devlog</h2>
<h3>[2022-01-11] SENPAI has hit release 1.0 !</h3>
<p>
It's been years since work started on SENPAI. Well, here it is. SENPAI
is fully usable as a molecular dynamics simulator.<br />
This doesn't mean it's done. There are still many features to be
added, like solvation, fully implementing models instead of the
current hardcoding... But this is it, SENPAI is usable. Have fun with
it, start poking around with, maybe send us some feedback. Either way,
thanks to the people around the world who have been supporting the
project since its inception in 2018.
</p>
</div>
</main>
</body>
</html>