normal martini topology for cyclopentane ring

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1 year 8 months ago #5483 by jmondal
jmondal created the topic: martini topology for cyclopentane ring
Hi
I wanted to know whether there is any martini parameters for cyclopentane rings. I am aware of the presence of cyclohexane ring parameters where they use 3 SC1 type beads to create a ring. Can someone suggest what will be a good approximation for cyclopentane coarse-grained ring ?

Thanks
Jagannath

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1 year 8 months ago #5484 by riccardo
riccardo replied the topic: martini topology for cyclopentane ring
Hi,
As far as I know, there aren't parameters for cyclopentane, so here what I can say about it.

It's a bit of a tricky molecule to parametrize because of the 5 carbon atoms is composed of which you would tend to map to 3 (SC1, or maybe SC2) beads to keep the ring planarity. That's the Martini way to go. However, like this you'll have a 5/3=1.6-to-1 mapping which start to go far also from the 3-to-1 or 2-to-1 mapping recommended for S-beads. So, I recommend you to check the partitioning of such a Martini model, and also the property of pure cyclopentane (it must be liquid at room T, and have a density in quite good agreement with the experimental one). I'd start using constraints between the 3 beads (as done for benzene).

Hope this helps,
Riccardo

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1 year 8 months ago #5485 by Pim
Pim replied the topic: martini topology for cyclopentane ring
Indeed. I'd say it depends a little bit what you want to use it for. If it's part of a bigger molecule, you might be able to group some more atoms from the substituents into the bead, like we did for cholesterol for example (it has 6-rings and 5-rings attached to each other), see www.rug.nl/research/portal/files/2923122...rols_jchemphys15.pdf . If you want to use it as a solvent for example, you're going to have to go with Riccardo's suggestion.

I've tried mapping it with 3 atoms in a ring as part of a fluorene group once, and it was particularly unstable, so if it wouldn't hurt your system too much, perhaps you could even let go of the ring-mapping.

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