/
index-1.html
269 lines (247 loc) · 13.1 KB
/
index-1.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
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
<!DOCTYPE html>
<html prefix="
og: http://ogp.me/ns#
article: http://ogp.me/ns/article#
" lang="en">
<head>
<meta charset="utf-8">
<meta name="description" content="Linux software for chemistry: molecular modeling, visualization, graphic, quantum mechanic, dynamic, kinetic, simulation">
<meta name="viewport" content="width=device-width">
<title>Linux4Chemistry (old posts, page 1) | Linux4Chemistry</title>
<link href="assets/css/all-nocdn.css" rel="stylesheet" type="text/css">
<link rel="alternate" type="application/rss+xml" title="RSS" href="rss.xml">
<link rel="canonical" href="https://linux4chemistry.github.io/index-1.html">
<!--[if lt IE 9]><script src="/assets/js/html5.js"></script><![endif]--><style>
div.input_prompt {
display: none;
}
</style>
</head>
<body>
<section class="social"><ul>
<li><a href="index.html" title="Home"><i class="icon-home"></i></a></li>
<li><a href="archive.html" title="Archives"><i class="icon-folder-open-alt"></i></a></li>
<li><a href="categories/index.html" title="Tags"><i class="icon-tags"></i></a></li>
<li><a href="rss.xml" title="RSS"><i class="icon-rss"></i></a></li>
<li><a href="stories/about.html" title="About linux4chemistry"><i class="icon-user"></i></a></li>
<li><a href="stories/definitions.html" title="Software licenses"><i class="icon-book"></i></a></li>
<li><a href="https://twitter.com/linux4chemistry" title="Twitter"><i class="icon-twitter"></i></a></li>
<li><a href="https://github.com/linux4chemistry/linux4chemistry.github.io" title="Github"><i class="icon-github"></i></a></li>
</ul></section><section class="page-content"><div class="content" rel="main">
<div class="post">
<h1 class="title"><a href="posts/xrdl.html">XRDL</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/crystallography.html" rel="tag">Crystallography</a></li>
</ul>
</div>
</div>
<div class="body">
<p>XRDL is reciprocal space viewer written in Java. It is also released as part of JSV. It allows real-time rotation of the reciprocal lattice points. This software is 'Charityware'.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/xvibs.html">XVibs</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/3d-viewer.html" rel="tag">3D Viewer</a></li>
<li><a class="tag p-category" href="categories/gpl.html" rel="tag">GPL</a></li>
<li><a class="tag p-category" href="categories/java.html" rel="tag">Java</a></li>
<li><a class="tag p-category" href="categories/quantum-mechanics.html" rel="tag">Quantum Mechanics</a></li>
</ul>
</div>
</div>
<div class="body">
<p>XVibs is a utility for animating molecular vibrations. Normal modes are read from a file automatically determined to be from Aces2, Gamess, PC Gamess, Gaussian 90/92/95/94/98, ADF, Dalton, Jaguar, MOPAC, or HyperChem. Separate animation files are written for each vibration.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/yaehmop.html">YAeHMOP</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/c.html" rel="tag">C</a></li>
<li><a class="tag p-category" href="categories/fortran.html" rel="tag">Fortran</a></li>
<li><a class="tag p-category" href="categories/gpl.html" rel="tag">GPL</a></li>
<li><a class="tag p-category" href="categories/quantum-mechanics.html" rel="tag">Quantum Mechanics</a></li>
</ul>
</div>
</div>
<div class="body">
<p>Yet Another extended Huckel Molecular Orbital Package (YAeHMOP) is intended to be an easy to use, transparent, extended Huckel calculation and visualization package which can perform calculations on both molecular and extended materials in 1,2, or 3 dimensions.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/yambo.html">Yambo</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/c.html" rel="tag">C</a></li>
<li><a class="tag p-category" href="categories/fortran.html" rel="tag">Fortran</a></li>
<li><a class="tag p-category" href="categories/gpl.html" rel="tag">GPL</a></li>
<li><a class="tag p-category" href="categories/quantum-mechanics.html" rel="tag">Quantum Mechanics</a></li>
</ul>
</div>
</div>
<div class="body">
<p>Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by the DFT codes abinit and Pwscf.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/yasara-dynamics.html">YASARA Dynamics</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/3d-viewer.html" rel="tag">3D Viewer</a></li>
<li><a class="tag p-category" href="categories/molecular-dynamics.html" rel="tag">Molecular Dynamics</a></li>
</ul>
</div>
</div>
<div class="body">
<p>YASARA Dynamics contains YASARA View and adds support for molecular simulations. Beside the YASARA NOVA Force Field and the new highly accurate YAMBER force fields, you can use other well known MD force fields like AMBER, and run accurate all-atom MD simulations in aqueous solution with Particle Mesh Ewald longrange electrostatics at twice the speed you know from other programs. YASARA Dynamics is not a black box with input and output files, but shows the MD simulation in real-time on screen. You can fully interact with the scene, pull atoms or whole molecules around.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/yasara-view.html">YASARA View</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/3d-viewer.html" rel="tag">3D Viewer</a></li>
</ul>
</div>
</div>
<div class="body">
<p>Explore macromolecular structures interactively with YASARA View, whose innotive 3D engine is up to 35 times faster than OpenGL. You can load multiple structures at the same time, create publication-quality ray-traced images including labels, and program your own macros and Python plugins.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/ymol.html">YMOL</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/3d-viewer.html" rel="tag">3D Viewer</a></li>
</ul>
</div>
</div>
<div class="body">
<p>Molecular visualisation and animation program, which can be used to create production quality images, and movies, using either the built in renderer or by exporting the scenes to POVRAY.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/zmm.html">ZMM</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/molecular-mechanics.html" rel="tag">Molecular Mechanics</a></li>
</ul>
</div>
</div>
<div class="body">
<p>ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes. ZMM searches optimal structures in the space of generalized coordinates: torsion angles, bond angles, bond lengths, positions of free molecules and ions, and orientation of free molecules.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/zodiac.html">Zodiac</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/c%2B%2B.html" rel="tag">C++</a></li>
<li><a class="tag p-category" href="categories/gpl.html" rel="tag">GPL</a></li>
</ul>
</div>
</div>
<div class="body">
<p>Zodiac is an advanced molecular editor for molecular modelling and computer aided drug design, that offers tools such as energy minimisation, database management, molecular property prediction and front ends to various docking and QM programs. It is cross platform and released under the GPL.</p>
</div>
</div>
<div class="post">
<h1 class="title"><a href="posts/zortep.html">ZORTEP</a></h1>
<div class="meta">
<div class="authordate">
<time class="timeago" datetime="2013-03-04T00:00:00+01:00">2013-03-04 00:00</time>
</div>
<div class="stats">
</div>
<div itemprop="keywords" class="tags">
<ul>
Tags :
<li><a class="tag p-category" href="categories/crystallography.html" rel="tag">Crystallography</a></li>
</ul>
</div>
</div>
<div class="body">
<p>ZORTEP is a mouse driven, menu based graphical ORTEP program. This allows the 'real-time' graphical rotation and manipulation of structures and/or thermal ellipsoids on the screen.</p>
</div>
</div>
<nav class="postindexpager"><ul class="pager">
<li class="previous">
<a href="index-2.html" rel="prev">Newer posts</a>
</li>
</ul></nav><footer id="footer"><p>Contents © 2017 <a href="mailto:ueb@linux4chemistry.info">l4c</a> - Powered by <a href="https://getnikola.com" rel="nofollow">Nikola</a> </p>
</footer>
</div>
</section><script src="assets/js/all-nocdn.js" type="text/javascript"></script><script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> </script><script type="text/x-mathjax-config">
MathJax.Hub.Config({tex2jax: {inlineMath: [['$latex ','$'], ['\\(','\\)']]}});
</script><script type="text/javascript">
$(function(){
$('.timeago').timeago();
});
</script>
</body>
</html>