normal About cis double bond in Lipid

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8 years 9 months ago #5011 by lsloneil
About cis double bond in Lipid was created by lsloneil
Hi,

I have a question about the cis double bond parameters in the lipid. Take the DIPC lipid as an example. In its itp file, I only saw bond angles set to 100 or 120 degrees to represent the unsaturated double bond configuration. However, according to my understanding, this is not enough to maintain a cis configuration since the molecule can be in trans configuration as well. I'm wondering if I would need some additional settings such as dihedral angles in order to maintain the cis configuration? For DIPC, I didn't see such dihedral angles.

Thanks.

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8 years 8 months ago #5237 by siewert
Replied by siewert on topic About cis double bond in Lipid
Hi,

at the atomistic level, dihedral angles are used to constrain a cis (or trans) configuration.

At the Martini level, these atomic details are lost, and the difference between cis/trans configuration is only captured effectively using an angle term between the beads surrounding the bead containing the double bond.

Siewert-Jan

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