-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmdtraj.html
145 lines (116 loc) · 5.36 KB
/
mdtraj.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
<!DOCTYPE html>
<html lang="en" prefix="og: http://ogp.me/ns# fb: https://www.facebook.com/2008/fbml">
<head>
<title>mdtraj - Yi Yao's Homepage</title>
<!-- Using the latest rendering mode for IE -->
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<link rel="canonical" href="./mdtraj.html">
<meta name="author" content="Yi Yao" />
<meta name="keywords" content="python" />
<meta name="description" content="mdtraj" />
<meta property="og:site_name" content="Yi Yao's Homepage" />
<meta property="og:type" content="article"/>
<meta property="og:title" content="mdtraj"/>
<meta property="og:url" content="./mdtraj.html"/>
<meta property="og:description" content="mdtraj"/>
<meta property="article:published_time" content="2014-12-02" />
<meta property="article:section" content="python" />
<meta property="article:tag" content="python" />
<meta property="article:author" content="Yi Yao" />
<!-- Bootstrap -->
<link rel="stylesheet" href="./themestatic/css/bootstrap.min.css" type="text/css"/>
<link href="./themestatic/css/font-awesome.min.css" rel="stylesheet">
<link href="./themestatic/css/pygments/native.css" rel="stylesheet">
<link rel="stylesheet" href="./themestatic/css/style.css" type="text/css"/>
</head>
<body>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-ex1-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a href="./" class="navbar-brand">
Yi Yao's Homepage </a>
</div>
<div class="collapse navbar-collapse navbar-ex1-collapse">
<ul class="nav navbar-nav">
<li><a href="index.html">About Me</a></li>
<li><a href="research.html">Research</a></li>
<li><a href="categories.html">Research Blogs</a></li>
</ul>
<ul class="nav navbar-nav navbar-right">
</ul>
</div>
<!-- /.navbar-collapse -->
</div>
</div> <!-- /.navbar -->
<!-- Banner -->
<!-- End Banner -->
<!-- Content Container -->
<div class="container">
<div class="row">
<div class="col-lg-12">
<section id="content">
<article>
<header class="page-header">
<h1>
<a href="./mdtraj.html"
rel="bookmark"
title="Permalink to mdtraj">
mdtraj
</a>
</h1>
</header>
<div class="entry-content">
<div class="panel">
<div class="panel-body">
<footer class="post-info">
<span class="label label-default">Date</span>
<span class="published">
<i class="fa fa-calendar"></i><time datetime="2014-12-02T16:08:00+01:00"> Tue 02 December 2014</time>
</span>
<span class="label label-default">Tags</span>
<a href="./tag/python.html">python</a>
</footer><!-- /.post-info --> </div>
</div>
<p>mdtraj is a python library to read, write and analyze MD trajectories. Here is its <a href="http://http://mdtraj.org">website</a>. It can be easy installed by conda and has the function to calculate distance for particles with periodic boundary conditions.</p>
<p>Here is how I use it on killdevil.</p>
<div class="highlight"><pre><span></span><code><span class="n">module</span> <span class="n">load</span> <span class="n">anaconda</span>
<span class="n">module</span> <span class="n">load</span> <span class="n">gcc</span><span class="o">/</span><span class="mf">4.8.1</span>
<span class="n">source</span> <span class="n">activate</span> <span class="n">my_root</span>
<span class="n">ipython</span>
<span class="kn">import</span> <span class="nn">mdtraj</span>
</code></pre></div>
</div>
<!-- /.entry-content -->
</article>
</section>
</div>
</div>
</div>
<!-- End Content Container -->
<footer>
<div class="container">
<hr>
<div class="row">
<div class="col-xs-10">© 2021 Yi Yao
· Powered by <a href="https://github.com/getpelican/pelican-themes/tree/master/pelican-bootstrap3" target="_blank">pelican-bootstrap3</a>,
<a href="http://docs.getpelican.com/" target="_blank">Pelican</a>,
<a href="http://getbootstrap.com" target="_blank">Bootstrap</a> </div>
<div class="col-xs-2"><p class="pull-right"><i class="fa fa-arrow-up"></i> <a href="#">Back to top</a></p></div>
</div>
</div>
</footer>
<script src="./themestatic/js/jquery.min.js"></script>
<!-- Include all compiled plugins (below), or include individual files as needed -->
<script src="./themestatic/js/bootstrap.min.js"></script>
<!-- Enable responsive features in IE8 with Respond.js (https://github.com/scottjehl/Respond) -->
<script src="./themestatic/js/respond.min.js"></script>
</body>
</html>