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Updated example 1 of msreact to work with the latest xtb version #13

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Updated example 1 of msreact to work with the latest xtb version #13

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bbeeb19
Updated example 1 of msreact to work with newest xtb version
gorges97 Apr 30, 2025
11b22c4
fixed typo
gorges97 Apr 30, 2025
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6 changes: 3 additions & 3 deletions page/examples/msreact-example_1.md
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Expand Up @@ -25,7 +25,8 @@ permalink: /page/examples/msreact/example_1.html
{% include image.html file="msreact-example-1-1.png" alt="Bacillaene at GFN-FF level" caption="Most stable gas-phase structure of 2-pentanone at charge +1 with GFN2-xTB." max-width=400 %}


We want to investigate the fragmentation reactions of 2-pentanone in an EI-MS experiment. Therefore, we provide the lowest conformer found by `CREST` at charge +1 as input <2-pentanone.xyz>. We only want to get unique fragments so we use the -msmolbar flag to sort out duplicates with `molbar`. Before starting crest, we should make sure that `molbar` is properly installed and can be executed globally.
We want to investigate the fragmentation reactions of 2-pentanone in an EI-MS experiment. Therefore, we need to specify the charge ('-chrg')
after the ionization and the number of unpaired electrons at the specific charge ('-uhf'). We provide the lowest conformer found by `CREST` at charge +1 as input <2-pentanone.xyz>. Since we only want to get unique fragments we use the -msmolbar flag to sort out duplicates with `molbar`. Before starting crest, we should make sure that `molbar` is properly installed and can be executed globally.
{: .text-justify }


Expand All @@ -38,8 +39,7 @@ We want to investigate the fragmentation reactions of 2-pentanone in an EI-MS ex
</div>
<!-- Tab content -->
<div id="tab-1-1" class="tabcontent tab-id-1" style="text-align:justify">
{% include command.html cmd='crest 2-pentanone.xyz <span class="nt">--msreact</span> <span class="nt">--chrg</span> 1 <span class="nt">--msmolbar</span> <span class="nt">--T</span> 16
' %}
{% include command.html cmd='crest 2-pentanone.xyz <span class="nt">--msreact</span> <span class="nt">--chrg</span> 1 <span class="nt">--uhf</span> 1 <span class="nt">--msmolbar</span> <span class="nt">--T</span> 16' %}
</div>

<div id="tab-1-2" class="tabcontent tab-id-1" style="text-align:justify">
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