| layout | title | parent | grand_parent | nav_order | toc | summary | permalink |
|---|---|---|---|---|---|---|---|
default |
TYR on graphene |
Publication Examples |
Examples and Guides |
3 |
false |
An example for conformers of tyrosine on a graphene cutout. |
/page/examples/publication/example_3.html |
{: .no_toc }
{{ page.summary }} {: .fs-6 .fw-300 }
To sample a tyrosine molecule at a graphene surface, the graphene sheet has to be constrained. All atoms in the graphene layer are constrained and removed from the metadynamics list. For a detailed guide on how to fix substructure parts see Example 4. {: .test-justify }
{% include image.html file="pub-example-3-1.png" alt="Tyrosine on graphene" caption="Tyrosine on a graphene cutout." max-width=300 %}
In order for the caluculation to be stable, some of the MD settings have to be adjusted.
The SHAKE constraint is turned off (--shake 0), the timestep is reduced to 1 fs (--tstep 1), and only the unconstrained atoms are included in the metadynamics bias and structure comparisons in CREGEN (--subrmsd).
{: .text-justify}
{{ site.data.icons.code }}
command
{{ site.data.icons.codefile }} coord/coord.ref
{{ site.data. icons.codefile }} constraints.inp
{% include command.html cmd='crest coord --subrmsd --shake 0 --tstep 1 --cinp constraints.inp' %}
{% capture struc_file %}
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$end
{% endcapture %}
{% include codecell.html content=struc_file style="font-size:10px" %}
{% capture struc_file %}
$constrain
atoms: 1-252
force constant=0.5
reference=coord.ref
$metadyn
atoms: 253-276
$end
{% endcapture %}
{% include codecell.html content=struc_file style="font-size:10px" %}
{% include defaulttab.html id="open-1" %}