unanswered Atom to bead mapping of alkyl chains

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6 months 3 weeks ago #9261 by Jassu
Hi everyone,

I am currently trying to parametrise a molecule, which has these alkyl side-chains with five and seven carbons.
The issue I face is how do I select the beads and map them to bead types?

As I'm using Martini 3, should I pick one larger bead and one smaller bead? And does the location of the smaller bead matter (on the exterior or closer to main chain) or would it be more accurate to use 2 same sized beads but bring them closer artificially?

Best,
Jassu

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