Molecular Dynamics Workshop Series, June 24-26, 2009

Simbios is excited to announce its Molecular Dynamics Workshop Series. The series consists of three workshops, showcasing software designed for individuals with different interests and experience with molecular dynamics (MD), from novices to experts.<b>OpenMM Developers Workshop:</b> Geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures, such as GPUs. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs, and has demonstrated speed ups of over 100X for implicit solvent simulations. The workshop will highlight the explicit solvent capabilities that will be available in the next OpenMM release (in June) and include a special track focused on integration of OpenMM into AMBER.<b>Introduction to Markov State Models and MSMBuilder:</b> For researchers who want to analyze MD simulations, mapping out the metastable states of a molecule and the transition rates between them. You will learn about Markov State Models and why they are suitable for this, and use the MSMBuilder software to automatically construct such models, as well as analyze and visualize them.<b>Introduction to Molecular Dynamics and OpenMM Zephyr:</b> For researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs.OpenMM and OpenMM Zephyr are accelerated only on specific NVIDIA and ATI GPU cards. <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=395#pack_673">Day 1 -- OpenMM </a> : Geared towards developers who are interested in using the OpenMM library to enable their MD code to run on high performance computer architectures, such as GPUs. The current version of the freely downloadable OpenMM enables MD codes to run on NVIDIA and ATI GPUs, and has demonstrated speed ups of over 100X for implicit solvent simulations.[1] </li> <li> <a href="https://simtk.org/frs?group_id=395#pack_674">Day 2 -- MSMBuilder </a> : For researchers who want to analyze MD simulations, mapping out the metastable states of a molecule and the transition rates between them. You will learn about Markov State Models and why they are suitable for this, and use the MSMBuilder software[2] to automatically construct such models, as well as analyze and visualize them. </li> <li> <a href="https://simtk.org/frs?group_id=395#pack_675">Day 3 -- MD & Zephyr </a> : For researchers interested in using MD in their research, including novices to MD. You will learn the theory behind MD and use the OpenMM Zephyr application, which makes it easy to run and visualize MD simulations. OpenMM Zephyr incorporates the OpenMM library, enabling acceleration of the simulations on GPUs. </li> <li> <a href="https://simtk.org/frs?group_id=395#pack_677">Other Workshop Information </a> </li> </ul>

Simbios欣然宣布其分子动力学研讨会系列。该系列包括三个研讨会，旨在展示适用于具有不同兴趣和分子动力学（MD）经验（从初学者到专家）的个人设计的软件。<b>OpenMM 开发者研讨会：</b>面向对使用 OpenMM 库以使其 MD 代码能够在高性能计算机架构（如 GPU）上运行的开发者。目前免费可下载的 OpenMM 版本使得 MD 代码能够在 NVIDIA 和 ATI GPU 上运行，并在隐式溶剂模拟中实现了超过 100 倍的速度提升。研讨会将重点介绍将在下一个月度 OpenMM 版本（六月）中提供的显式溶剂功能，并包含一个专注于 OpenMM 与 AMBER 集成的特别轨道。<b>马尔可夫状态模型与 MSMBuilder 简介：</b>面向希望分析 MD 模拟、绘制分子亚稳态及其相互间转换速率的研究者。您将了解马尔可夫状态模型及其为何适用于此的原因，并使用 MSMBuilder 软件[2]自动构建此类模型，以及对其进行分析和可视化。<b>分子动力学与 OpenMM Zephyr 简介：</b>面向对在研究中使用 MD 感兴趣的研究者，包括 MD 初学者。您将学习 MD 的理论背景，并使用 OpenMM Zephyr 应用程序，该程序使得运行和可视化 MD 模拟变得简便。OpenMM Zephyr 集成了 OpenMM 库，使得 GPU 上的模拟加速成为可能。OpenMM 和 OpenMM Zephyr 仅在特定的 NVIDIA 和 ATI GPU 卡上加速。此外，本项目包含以下软件/数据包：<br> <ul> <li> &lt;a href=&quot;https://simtk.org/frs?group_id=395#pack_673&quot;&gt;第一天 -- OpenMM &lt;/a&gt; : 面向对使用 OpenMM 库以使其 MD 代码能够在高性能计算机架构（如 GPU）上运行的开发者。目前免费可下载的 OpenMM 版本使得 MD 代码能够在 NVIDIA 和 ATI GPU 上运行，并在隐式溶剂模拟中实现了超过 100 倍的速度提升。[1] &lt;/li> <li> &lt;a href=&quot;https://simtk.org/frs?group_id=395#pack_674&quot;&gt;第二天 -- MSMBuilder &lt;/a&gt; : 面向希望分析 MD 模拟、绘制分子亚稳态及其相互间转换速率的研究者。您将了解马尔可夫状态模型及其为何适用于此的原因，并使用 MSMBuilder 软件[2]自动构建此类模型，以及对其进行分析和可视化。 &lt;/li> <li> &lt;a href=&quot;https://simtk.org/frs?group_id=395#pack_675&quot;&gt;第三天 -- MD &amp;amp; Zephyr &lt;/a&gt; : 面向对在研究中使用 MD 感兴趣的研究者，包括 MD 初学者。您将学习 MD 的理论背景，并使用 OpenMM Zephyr 应用程序，该程序使得运行和可视化 MD 模拟变得简便。OpenMM Zephyr 集成了 OpenMM 库，使得 GPU 上的模拟加速成为可能。 &lt;/li> <li> &lt;a href=&quot;https://simtk.org/frs?group_id=395#pack_677&quot;&gt;其他研讨会信息 &lt;/a&gt; &lt;/li> &lt;/ul>