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read/write lammps molecule templates #15

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7fe6e92
read/write molecule templates
jrgissing Aug 17, 2018
b6c7c23
update docs
jrgissing Sep 23, 2018
cc323f1
Update index.html
jrgissing Jan 23, 2021
d42badc
Merge branch 'master' of https://github.com/akohlmey/topotools into a…
jrgissing Jan 23, 2021
3ffab11
t push origin masterMerge branch 'akohlmey-master'
jrgissing Jan 23, 2021
5b99f3b
Merge branch 'master' into master
jrgissing Sep 23, 2023
bf17560
add support for Molecules section
jrgissing Oct 10, 2024
2f51ebd
fix writelammpsmol
jrgissing Oct 10, 2024
8f2749c
docs
jrgissing Oct 10, 2024
4cb6d63
docs fix
jrgissing Oct 10, 2024
7102f4e
docs fix
jrgissing Oct 10, 2024
3f8c9e1
last fix?
jrgissing Oct 10, 2024
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28 changes: 17 additions & 11 deletions doc/index.html
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Expand Up @@ -53,9 +53,11 @@
<ul class="goog-toc" style="list-style: none;">
<li class="goog-toc"><a href="#TOC-readlammpsdata-file-name-atom-style"><strong>4.1 </strong>readlammpsdata &lt;file name&gt; [&lt;atom style&gt;]</a></li>
<li class="goog-toc"><a href="#TOC-writelammpsdata-file-name-atom-styl"><strong>4.2 </strong>writelammpsdata &lt;file name&gt; [typelabels] [&lt;atom style&gt;]</a></li>
<li class="goog-toc"><a href="#TOC-readvarxyz-file-name-"><strong>4.3 </strong>readvarxyz &lt;file name&gt;</a></li>
<li class="goog-toc"><a href="#TOC-writevarxyz-file-name-selmod-sel-fi"><strong>4.4 </strong>writevarxyz &lt;file name&gt; [selmod &lt;sel&gt;] [first|last|step &lt;frame]</a></li>
<li class="goog-toc"><a href="#TOC-writegmxtop-file-name-"><strong>4.5 </strong>writegmxtop &lt;file name&gt;</a></li>
<li class="goog-toc"><a href="#TOC-readlammpsmol-file-name"><strong>4.3 </strong>readlammpsmol &lt;file name&gt; </a></li>
<li class="goog-toc"><a href="#TOC-writelammpsmol-file-name"><strong>4.4 </strong>writelammpsmol &lt;file name&gt; [typelabels]</a></li>
<li class="goog-toc"><a href="#TOC-readvarxyz-file-name-"><strong>4.5 </strong>readvarxyz &lt;file name&gt; [first|last|step &lt;frame] </a></li>
<li class="goog-toc"><a href="#TOC-writevarxyz-file-name-selmod-sel-fi"><strong>4.6 </strong>writevarxyz &lt;file name&gt; [selmod &lt;sel&gt;] [first|last|step &lt;frame]</a></li>
<li class="goog-toc"><a href="#TOC-writegmxtop-file-name-"><strong>4.7 </strong>writegmxtop &lt;file name&gt;</a></li>
</ul>
</li>
<li class="goog-toc"><a href="#TOC-Utility-Functions"><strong>5 </strong>Utility Functions</a>
Expand All @@ -77,7 +79,7 @@ <h3><a name="TOC-Scope-and-usage"></a>Scope and usage</h3>
topology data or even building topologies from scratch. The focus lies
hereby on being able to perform many operations manually or scripted and
thus being less focused on and optimized for biomolecules like
psfgen.</p>
psfgen.</p>
<p align="justify">In combination with the new command
<tt><code>mol new atoms &lt;number&gt;</code></tt> it is now also
possible to do many operations directly that previously required writing
Expand All @@ -86,7 +88,7 @@ <h3><a name="TOC-Scope-and-usage"></a>Scope and usage</h3>
is especially useful for file formats, where additional input from the
user is required, for example reading LAMMPS format "data" (=topology)
files, where the "style" of the<i>Atoms</i> section cannot be deduced
from the data. Of course write support is also possible.</p>
from the data. Of course write support is also possible.</p>
<p align="justify">The underlying Tcl script API in VMD itself had been
designed to be minimalistic, since most operations are not
computationally demanding and could be programmed with scripting. The
Expand All @@ -95,11 +97,11 @@ <h3><a name="TOC-Scope-and-usage"></a>Scope and usage</h3>
multiple low lever commands in a way to solve common tasks conveniently
and efficiently.</p>
<p align="justify">Finally <b>topotools</b> also contains some utilities and
applications for more complex operations like combining multiple molecules
applications for more complex operations like combining multiple molecules
(=different files) or multiple selections into one new molecule, or building
larger systems by replicating a given unitcell.</p>
<p align="justify">Updates and bug fixes for topotools between VMD releases
are available from <a href="https://sites.google.com/site/akohlmey/software/topotools">https://sites.google.com/site/akohlmey/software/topotools</a>.
are available from <a href="https://sites.google.com/site/akohlmey/software/topotools">https://sites.google.com/site/akohlmey/software/topotools</a>.
This page also links to a set of tutorial examples that demonstrate in more
detail, how the commands in the plugin can be used to build topology
data files for different kinds of MD simulation packages.</p>
Expand Down Expand Up @@ -211,7 +213,11 @@ <h4><a name="TOC-readlammpsdata-file-name-atom-style"></a>readlammpsdata &lt;fil
<p align="justify">Read in atom coordinates, properties, bond, angle, dihedral and other related topology info from a <a href="https://docs.lammps.org/read_data.html" target="_blank" rel="nofollow">LAMMPS</a> data file, i.e. a file suitable for the <code>read_data</code> command. This can be used to check a data file for its validity, for manipulations from within VMD, or to generate a .psf file to be used for visualization of <code>.dcd</code> or <code>.xtc</code> format trajectory files in VMD. The 'atom style' is the value given to the <code>atom_style</code> command in the LAMMPS input file (by default TopoTools will try to infer the atom style from information embedded in the data file as comments; if no such hints are present, it will use 'full'). This subcommand creates a new molecule in VMD and returns its molecule id or -1 in case of failure. The -sel parameter is currently ignored.</p>
<h4><a name="TOC-writelammpsdata-file-name-atom-styl"></a>writelammpsdata &lt;file name&gt; [typelabels] [&lt;atom style&gt;]</h4>
<p align="justify">Write out atom coordinates, properties, bond, angle, dihedral and other related topology info stored inside VMD to a <a href="https://docs.lammps.org/read_data.html" target="_blank" rel="nofollow">LAMMPS</a> data file, i.e. a file suitable for the <code>read_data</code> command. Using the optional 'typelabels' flag will trigger writing a data file with typelabel support requiring LAMMPS version 15Sep2022 or later. By default a traditional data file with numerical types will be written. This this way VMD can be used to build LAMMPS input with Tcl scripting and convert existing inputs from other MD codes to be used in LAMMPS. For some examples, please see the <a href="https://sites.google.com/site/akohlmey/software/topotools/tutorial-introduction">TopoTools tutorials</a>. The 'atom style' is the value you want to give to the <code>atom_style</code> command in the LAMMPS input file (default is 'full'). Only data that is present will be written and non-zero box sizes are required.</p>
<h4><a name="TOC-readvarxyz-file-name-"></a>readvarxyz &lt;file name&gt;</h4>
<h4><a name="TOC-readlammpsmol-file-name"></a>readlammpsmol &lt;file name&gt; </h4>
<p align="justify">Read in atom coordinates, properties, bond, angle, dihedral and other related topology info from a <a href="https://docs.lammps.org/molecule.html" target="_blank" rel="nofollow">LAMMPS</a> molecule template file, i.e. a file suitable for the <code>molecule</code> command. This can be used to check a molecule template for its validity (e.g. for fixes that utilize molecule templates), or for manipulations from within VMD. This subcommand creates a new molecule in VMD and returns its molecule id or -1 in case of failure. The -sel parameter is currently ignored.</p>
<h4><a name="TOC-writelammpsmol-file-name"></a>writelammpsmol &lt;file name&gt; [typelabels]</h4>
<p align="justify">Write out atom coordinates, properties, bond, angle, dihedral and other related topology info stored inside VMD to a <a href="https://docs.lammps.org/molecule.html" target="_blank" rel="nofollow">LAMMPS</a> molecule template file, i.e. a file suitable for the <code>molecule</code> command. Using the optional 'typelabels' flag will trigger writing a molecule template file with typelabel support requiring LAMMPS version 15Sep2022 or later. By default a traditional molecule template with numerical types will be written. This way VMD can be used to build LAMMPS input with Tcl scripting and convert existing inputs from other MD codes to be used in LAMMPS. Only data that is present will be written.</p>
<h4><a name="TOC-readvarxyz-file-name-"></a>readvarxyz &lt;file name&gt; [first|last|step &lt;frame]</h4>
<p align="justify">Read in an xyz-format trajectory file (in xmol style) with a varying number of atoms per frame. This format is normally not supported in VMD and the script circumvents the restriction by automatically adding a sufficient number of dummy particles. Whether an atom is actually present in a given frame or not is flagged by the value of the corresponding <code>user</code> field, which is set to either <code>1.0</code> or <code>-1.0</code>, respectively. For efficiency reasons the atoms are sorted by type, thus atom order and bonding is not preserved. This subcommand creates a new molecule and returns its molecule id or -1, in case of failure.</p>
<h4><a name="TOC-writevarxyz-file-name-selmod-sel-fi"></a>writevarxyz &lt;file name&gt; [selmod &lt;sel&gt;] [first|last|step &lt;frame]</h4>
<div>Write out an xyz-format trajectory file with a varying number of atoms per frame. This is the counterpart to the readvarxyz subcommand. The optional selection string defines how atoms for each frame have to be selected. If not given, as selection string of "user &gt; 0" is assumed.</div>
Expand Down Expand Up @@ -243,7 +249,7 @@ <h4><a name="TOC-selections2mol-list-of-atom-selecti"></a>selections2mol &lt;lis
<div><code>set sel [atomselect 0 protein]</code></div>
<div><code>lappend sellist $sel</code></div>
<div><code>set sel [atomselect 0 protein]</code></div>
<div><code>$sel frame 200 </code></div>
<div><code>$sel frame 200 </code></div>
<div><code>$sel moveby {50.0 50.0 0.0}</code></div>
<div><code>lappend sellist $sel</code></div>
<div><code>set sel [atomselect 1 "same residue as (within 3.0 of chain L)"]</code></div>
Expand All @@ -259,8 +265,8 @@ <h4><a name="TOC-replicatemol-mol-nx-ny-nz-"></a>replicatemol &lt;mol&gt; &lt;nx
<div class="sites-codeblock sites-codesnippet-block"><code>package require topotools 1.5 </code><div><code># load a molecule</code></div><div><code>set mol [mol new pegc12e8-small.xml type hoomd waitfor all]</code></div><div><code># do the magic</code></div><div><code>set newmol [::TopoTools::replicatemol $mol 2 2 1 ]</code></div><div><code>animate write hoomd replicated.xml $newmol</code></div></div>
<div><br />
</div></div></td></tr></tbody></table>
</div>
</div>
</div>
</div>

<h3 ><a name="TOC-Author"></a>Author</h3>
<p><a href="https://sites.google.com/site/akohlmey/">Axel Kohlmeyer</a> with contributions from Josh Vermaas (TopoGromacs, i.e. fully working gromacs topology files for CHARMM style parameter files) and Konstantin W (replicatemols for non-orthogonal cells) </p>
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