TYR on graphene
An example for conformers of tyrosine on a graphene cutout.
Conformational sampling of tyrosine on a graphene surface
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.
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).
crest coord --subrmsd --shake 0 --tstep 1 --cinp constraints.inp
$coord
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$end
$constrain
atoms: 1-252
force constant=0.5
reference=coord.ref
$metadyn
atoms: 253-276
$end