normal Van der Waals radius of the bead.

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9 years 8 months ago - 9 years 8 months ago #3973 by initram
Van der Waals radius of the bead. was created by initram
Hi,

I can't find the default radii of the Martini CG beads!

On the webpage "Martini tutorials:lipids" under "Bilayer self assembly" I see that default value of 0.105 nm was changed to 0.21 nm in order "to reflect the size of the Martini CG beads" when water was added to the system. My question is: why this change was not performed in the first step (minimization step) before water was added?
Where can I find the default radii of the Martini CG beads?

Thank you
Last edit: 9 years 8 months ago by initram.

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9 years 8 months ago #3974 by Clement
Replied by Clement on topic Van der Waals radius of the bead.
The radii of martini beads is effectively defined by the minimal value of the van der Waals potential (giving the diameter): for regular beads it is around 0.26 nm (0.52/2), for S-beads around 0.23 nm (0.47/2).

Changing the -vdw flag to 0.21 is just a trick when solvating the mixture of lipids; it avoids clashes and high forces when minimizing the whole system (including water). This does not set any properties of the Martini beads...

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9 years 8 months ago #3981 by initram
Replied by initram on topic Van der Waals radius of the bead.
Hi,

Thank you very much for the answer.

BR

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