Skip to content

Commit

Permalink
Site updated: 2024-12-17 22:36:04
Browse files Browse the repository at this point in the history
  • Loading branch information
@shaoqx
shaoqx committed Dec 18, 2024
1 parent 7563dca commit ac2540c
Show file tree
Hide file tree
Showing 9 changed files with 17 additions and 9 deletions.
10 changes: 9 additions & 1 deletion 2020/11/16/Amber-MD关键字/index.html
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<!doctype html>
<html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1"><meta><title>Amber MD关键字 - NOTES and REFS</title><link rel="manifest" href="/manifest.json"><meta name="application-name" content="NOTES and REFS"><meta name="msapplication-TileImage" content="/img/avatar.png"><meta name="apple-mobile-web-app-capable" content="yes"><meta name="apple-mobile-web-app-title" content="NOTES and REFS"><meta name="apple-mobile-web-app-status-bar-style" content="default"><meta description="之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。"><meta property="og:type" content="blog"><meta property="og:title" content="Amber MD关键字"><meta property="og:url" content="http://yoursite.com/2020/11/16/Amber-MD%E5%85%B3%E9%94%AE%E5%AD%97/"><meta property="og:site_name" content="NOTES and REFS"><meta property="og:description" content="之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。"><meta property="og:locale" content="en_US"><meta property="og:image" content="http://yoursite.com/images/iwarp.png"><meta property="article:published_time" content="2020-11-16T23:41:26.000Z"><meta property="article:modified_time" content="2024-12-18T04:33:30.226Z"><meta property="article:author" content="shaoqz"><meta property="article:tag" content="chinese"><meta property="article:tag" content="Amber"><meta property="article:tag" content="MD"><meta property="article:tag" content="MMPBSA"><meta property="article:tag" content="MCPB"><meta property="twitter:card" content="summary"><meta property="twitter:image" content="/images/iwarp.png"><script type="application/ld+json">{"@context":"https://schema.org","@type":"BlogPosting","mainEntityOfPage":{"@type":"WebPage","@id":"http://yoursite.com/2020/11/16/Amber-MD%E5%85%B3%E9%94%AE%E5%AD%97/"},"headline":"NOTES and REFS","image":["http://yoursite.com/images/iwarp.png"],"datePublished":"2020-11-16T23:41:26.000Z","dateModified":"2024-12-18T04:33:30.226Z","author":{"@type":"Person","name":"shaoqz"},"description":"之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。"}</script><link rel="canonical" href="http://yoursite.com/2020/11/16/Amber-MD%E5%85%B3%E9%94%AE%E5%AD%97/"><link rel="icon" href="/img/avatar.png"><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.12.0/css/all.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/styles/atom-one-light.css"><link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Ubuntu:wght@400;600&amp;family=Source+Code+Pro"><link rel="stylesheet" href="/css/default.css"><style>body>.footer,body>.navbar,body>.section{opacity:0}</style><!--!--><!--!--><!--!--><!--!--><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/build/cookieconsent.min.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/lightgallery.min.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/justifiedGallery.min.css"><!--!--><!--!--><!--!--><script src="https://cdn.jsdelivr.net/npm/[email protected]/pace.min.js"></script><!--!--><!--!--><meta name="generator" content="Hexo 5.0.2"></head><body class="is-2-column"><nav class="navbar navbar-main"><div class="container"><div class="navbar-brand justify-content-center"><a class="navbar-item navbar-logo" href="/">SHAOQZ.CN</a></div><div class="navbar-menu"><div class="navbar-start"><a class="navbar-item" href="/">Home</a><a class="navbar-item" href="/archives">Archives</a><a class="navbar-item" href="/categories">Categories</a><a class="navbar-item" href="/tags">Tags</a><a class="navbar-item" href="/ref-rank">Paper Ranking</a></div><div class="navbar-end"><a class="navbar-item" target="_blank" rel="noopener" title="GitHub" href="https://github.com/shaoqx"><i class="fab fa-github"></i></a><a class="navbar-item is-hidden-tablet catalogue" title="Catalogue" href="javascript:;"><i class="fas fa-list-ul"></i></a><a class="navbar-item search" title="Search" href="javascript:;"><i class="fas fa-search"></i></a></div></div></div></nav><section class="section"><div class="container"><div class="columns"><div class="column order-2 column-main is-8-tablet is-8-desktop is-8-widescreen"><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted&nbsp;<time dateTime="2020-11-16T23:41:26.000Z" title="2020-11-16T23:41:26.000Z">2020-11-16</time></span><span class="level-item">Updated&nbsp;<time dateTime="2024-12-18T04:33:30.226Z" title="2024-12-18T04:33:30.226Z">2024-12-17</time></span><span class="level-item"><a class="link-muted" href="/categories/Notes/">Notes</a><span> / </span><a class="link-muted" href="/categories/Notes/Tools/">Tools</a></span><span class="level-item">an hour read (About 8614 words)</span></div></div><h1 class="title is-3 is-size-4-mobile">Amber MD关键字</h1><div class="content"><p>之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。</p>
<html lang="en"><head><meta charset="utf-8"><meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=1"><meta><title>Amber MD关键字 - NOTES and REFS</title><link rel="manifest" href="/manifest.json"><meta name="application-name" content="NOTES and REFS"><meta name="msapplication-TileImage" content="/img/avatar.png"><meta name="apple-mobile-web-app-capable" content="yes"><meta name="apple-mobile-web-app-title" content="NOTES and REFS"><meta name="apple-mobile-web-app-status-bar-style" content="default"><meta description="之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。"><meta property="og:type" content="blog"><meta property="og:title" content="Amber MD关键字"><meta property="og:url" content="http://yoursite.com/2020/11/16/Amber-MD%E5%85%B3%E9%94%AE%E5%AD%97/"><meta property="og:site_name" content="NOTES and REFS"><meta property="og:description" content="之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。"><meta property="og:locale" content="en_US"><meta property="og:image" content="http://yoursite.com/images/iwarp.png"><meta property="article:published_time" content="2020-11-16T23:41:26.000Z"><meta property="article:modified_time" content="2024-12-18T04:35:59.647Z"><meta property="article:author" content="shaoqz"><meta property="article:tag" content="chinese"><meta property="article:tag" content="Amber"><meta property="article:tag" content="MD"><meta property="article:tag" content="MMPBSA"><meta property="article:tag" content="MCPB"><meta property="twitter:card" content="summary"><meta property="twitter:image" content="/images/iwarp.png"><script type="application/ld+json">{"@context":"https://schema.org","@type":"BlogPosting","mainEntityOfPage":{"@type":"WebPage","@id":"http://yoursite.com/2020/11/16/Amber-MD%E5%85%B3%E9%94%AE%E5%AD%97/"},"headline":"NOTES and REFS","image":["http://yoursite.com/images/iwarp.png"],"datePublished":"2020-11-16T23:41:26.000Z","dateModified":"2024-12-18T04:35:59.647Z","author":{"@type":"Person","name":"shaoqz"},"description":"之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。"}</script><link rel="canonical" href="http://yoursite.com/2020/11/16/Amber-MD%E5%85%B3%E9%94%AE%E5%AD%97/"><link rel="icon" href="/img/avatar.png"><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.12.0/css/all.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/styles/atom-one-light.css"><link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Ubuntu:wght@400;600&amp;family=Source+Code+Pro"><link rel="stylesheet" href="/css/default.css"><style>body>.footer,body>.navbar,body>.section{opacity:0}</style><!--!--><!--!--><!--!--><!--!--><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/build/cookieconsent.min.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/lightgallery.min.css"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/justifiedGallery.min.css"><!--!--><!--!--><!--!--><script src="https://cdn.jsdelivr.net/npm/[email protected]/pace.min.js"></script><!--!--><!--!--><meta name="generator" content="Hexo 5.0.2"></head><body class="is-2-column"><nav class="navbar navbar-main"><div class="container"><div class="navbar-brand justify-content-center"><a class="navbar-item navbar-logo" href="/">SHAOQZ.CN</a></div><div class="navbar-menu"><div class="navbar-start"><a class="navbar-item" href="/">Home</a><a class="navbar-item" href="/archives">Archives</a><a class="navbar-item" href="/categories">Categories</a><a class="navbar-item" href="/tags">Tags</a><a class="navbar-item" href="/ref-rank">Paper Ranking</a></div><div class="navbar-end"><a class="navbar-item" target="_blank" rel="noopener" title="GitHub" href="https://github.com/shaoqx"><i class="fab fa-github"></i></a><a class="navbar-item is-hidden-tablet catalogue" title="Catalogue" href="javascript:;"><i class="fas fa-list-ul"></i></a><a class="navbar-item search" title="Search" href="javascript:;"><i class="fas fa-search"></i></a></div></div></div></nav><section class="section"><div class="container"><div class="columns"><div class="column order-2 column-main is-8-tablet is-8-desktop is-8-widescreen"><div class="card"><article class="card-content article" role="article"><div class="article-meta is-size-7 is-uppercase level is-mobile"><div class="level-left"><span class="level-item">Posted&nbsp;<time dateTime="2020-11-16T23:41:26.000Z" title="2020-11-16T23:41:26.000Z">2020-11-16</time></span><span class="level-item">Updated&nbsp;<time dateTime="2024-12-18T04:35:59.647Z" title="2024-12-18T04:35:59.647Z">2024-12-17</time></span><span class="level-item"><a class="link-muted" href="/categories/Notes/">Notes</a><span> / </span><a class="link-muted" href="/categories/Notes/Tools/">Tools</a></span><span class="level-item">an hour read (About 8614 words)</span></div></div><h1 class="title is-3 is-size-4-mobile">Amber MD关键字</h1><div class="content"><p>之前了解了一遍Amber动力学输入文件中关键字的含义，但是几个月不用再一看又不熟悉了。为此做一个方便快速检索参考的中文笔记。</p>
<a id="more"></a>
<hr>
<h1 id="MD模拟"><a href="#MD模拟" class="headerlink" title="MD模拟"></a>MD模拟</h1><hr>
Expand Down Expand Up @@ -429,26 +429,32 @@ <h3 id="4-在每个窗口进行MD模拟"><a href="#4-在每个窗口进行MD模
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">DUMPAVE&#x3D;dihedral_60.dat</span><br></pre></td></tr></table></figure>
<p>部分从而直接输出采样得到的constraint的值</p>
<p><font color=gray size=2>貌似不进行heating了，不过heating本身的必要性也不明确 (<a target="_blank" rel="noopener" href="https://github.com/openmm/openmm/issues/4240">https://github.com/openmm/openmm/issues/4240</a>)</font></p>
<hr>
<h4 id="运行时长"><a href="#运行时长" class="headerlink" title="运行时长"></a>运行时长</h4><p>需要模拟足够长时间从而保证该约束条件下的采样收敛</p>
<p>理想情况下被约束的坐标自己往往涉及较大时间尺度的变化而其余的坐标可以在可接受的模拟时间尺度内收敛</p>
<p>*官方教程建议采样完成后随机去除20%的数据再计算一次PMF来验证其收敛</p>
<hr>
<h4 id="初始结构"><a href="#初始结构" class="headerlink" title="初始结构"></a>初始结构</h4><p>初始结构在路径坐标上的值不宜与约束的目标值相差太大（例如：初始结构为1A 约束在10A）</p>
<p>但是也需要尽可能地平行提交计算任务</p>
<p>常用的策略是手动创建一些中间点的初始结构之后从这些结构开始</p>
<p>或者使顺序运行逐步改变初始结构</p>
<hr>
<h4 id="验证采样结果"><a href="#验证采样结果" class="headerlink" title="验证采样结果"></a>验证采样结果</h4><p>可以做出采样结果在路径坐标上的histogram来判断设置是否有效</p>
<ul>
<li>重叠是否充分</li>
<li>采样是否全面</li>
</ul>
<hr>
<h3 id="5-用WHAM分析结果"><a href="#5-用WHAM分析结果" class="headerlink" title="5. 用WHAM分析结果"></a>5. 用WHAM分析结果</h3><blockquote>
<p>使用 Alan Grossfield 开发的WHAM程序 </p>
<p><a target="_blank" rel="noopener" href="http://membrane.urmc.rochester.edu/?page_id=126">http://membrane.urmc.rochester.edu/?page_id=126</a></p>
</blockquote>
<hr>
<h4 id="5-1-安装WHAM"><a href="#5-1-安装WHAM" class="headerlink" title="5.1 安装WHAM"></a>5.1 安装WHAM</h4><p>从Alan Grossfield的官网上下载源代码(<a target="_blank" rel="noopener" href="http://membrane.urmc.rochester.edu/?page_id=126/">http://membrane.urmc.rochester.edu/?page_id=126/</a>)</p>
<p>参考manual安装</p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">tar -xvf wham-release-#####.tgz </span><br><span class="line">cd wham&#x2F;wham</span><br><span class="line">make clean</span><br><span class="line">make</span><br></pre></td></tr></table></figure>
<p><font color=red size=2>注意截至2.0.11版本，WHAM的编译仍不支持GCC 10.2.0，调整环境至GCC 8.2.0方编译成功</font></p>
<hr>
<h4 id="5-2-运行WHAM"><a href="#5-2-运行WHAM" class="headerlink" title="5.2 运行WHAM"></a>5.2 运行WHAM</h4><figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">&#123;dir_of_wham&#125;&#x2F;wham [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad metadatafile freefile [num_MC_trials randSeed]</span><br></pre></td></tr></table></figure>

<ul>
Expand All @@ -474,7 +480,9 @@ <h4 id="5-2-运行WHAM"><a href="#5-2-运行WHAM" class="headerlink" title="5.2
<li><code>correl time</code> 只在Monte Carlop bootstrap 错误分析时使用指定该采样集合的相关时间</li>
<li><code>temperature</code> 如果指定覆盖命令行指定的温度</li>
</ul>
<hr>
<h4 id="5-3-分析WHAM结果"><a href="#5-3-分析WHAM结果" class="headerlink" title="5.3 分析WHAM结果"></a>5.3 分析WHAM结果</h4><p>WHAM的结果为坐标和自由能，直接作图分析</p>
<hr>
<h1 id="Misc-1"><a href="#Misc-1" class="headerlink" title="Misc"></a>Misc</h1><h2 id="tleap"><a href="#tleap" class="headerlink" title="tleap"></a>tleap</h2><p>tleap自动加氢甚至不会考虑周围的金属离子(如Zn2+等配位中心)，会把旁边的残基质子化而不考虑配位</p>
<h2 id="prepin格式"><a href="#prepin格式" class="headerlink" title="prepin格式"></a>prepin格式</h2><blockquote>
<p><a target="_blank" rel="noopener" href="https://ambermd.org/doc/prep.html">https://ambermd.org/doc/prep.html</a><br>利用树和LOOP的方式描述连接</p>
Expand Down
Loading

0 comments on commit ac2540c

Please sign in to comment.