normal Cyclohexane in Martini 3

  • aleme
  • aleme's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
3 years 4 months ago #8803 by aleme
Cyclohexane in Martini 3 was created by aleme
Dear all,

I see that in the topology file for solvents in Martini 3 cyclohexane is reproduced by 2 beads (SC3) and in Martini 2 cyclohexane was mapped with 3 beads (SC1). Is there a particular reason for the change from 3 to 2 beads in the new parameterization?
Given that the molecule is cyclic and similar to benzene, which is reproduced with 3 beads, I don't understand why there are only 2 beads.

Thank you in advance!

Best regards,
Aleksandar

Please Log in or Create an account to join the conversation.

More
3 years 3 months ago #8816 by riccardo
Replied by riccardo on topic Cyclohexane in Martini 3
Hi Aleksandar,
The rationale behind the choice is the following. Cyclohexane (CHEX) is aliphatic: due to the presence of 2 hydrogen atoms per carbon and its non-flat structure, CHEX is a bulkier ring than benzene. In Martini 3, small beads capture this bulkiness better than tiny beads, and small beads have been parametrized to represent 3 non-hydrogen atoms. These 2 factors call for a model for CHEX consisting of two small-beads (2 SC3 beads to be precise, as you note). Tiny beads are instead optimal for aromatic structures since they are "atom-thick", i.e., their sigma is comparable to the one of carbon atoms in an atomistic force field, so that you can obtain stacking distances between aromatics in agreement with all-atom force fields (and experiments). Since tiny beads were parametrized to represent 2 non-hydrogen atoms, you need 3 tiny beads to model benzene. 
Hope this helps!
Riccardo

Please Log in or Create an account to join the conversation.

  • aleme
  • aleme's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
3 years 3 months ago #8824 by aleme
Replied by aleme on topic Cyclohexane in Martini 3
Hi Riccardo,

This makes sense. Thank you for the explanation!

Best regards,
Aleksandar

Please Log in or Create an account to join the conversation.

Time to create page: 0.083 seconds