normal how to mapping triple bond?

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10 years 5 months ago #2300 by always2323
how to mapping triple bond? was created by always2323
Hi. I have used grimaces 4.5.3 with martini force field. I'm familiar with martini force field and procedure.

however, I have a problem with mapping method related to carbon- carbon triple bond.

In martini force field, there are two examples concerned single and cis, trans-double bond.

My question is - Can I use 180 bond angle with proper force constant in order to describe residue with carbon-carbon triple bond?

In comparison with COM of Atomic simulation, it didn't show 180 degree.

Is there any example or recommendation ?

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10 years 5 months ago - 10 years 5 months ago #2473 by xavier
Replied by xavier on topic how to mapping triple bond?
A triple bond would indeed be straight and thus a 180 degrees angle should be fine but you'll have to consider the increase in polarity of the bond. This should be included in the bead type.

I actually believe there is an example of a triple bond in the original MARTINI topology ... check the Marrink-2007 paper. The bead type was C4 for a butyne C2-C2 where - is a triple bond.

In regards the angle value it is not clear what your mean. But you'd have to play with the angle used in the CG topology to reproduce the atomistic distribution.
Last edit: 10 years 5 months ago by xavier.

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