normal what is the difference between elastic network model and elnedyn?

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9 years 3 months ago #1401 by junfeng
In the martinize.py, we have options to choose elastic network or elnedyn. What is the difference? Both apply harmonic potential to constraint equilibrium distances between beads. But I notice certain bond constraints are not applied in elnedyn. Can anyone explain the detailed difference? methodologically?

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9 years 3 months ago #1402 by djurre
There are several differences. An elastic network simply defines elastic bonds between the beads of Martini structure with the force constant you give. Elnedyn changes more things, specified in "Periole et al. 2009, DOI:10.1021/ct9002114). The most important changes are: BB beads are positioned at the Calpha instead of COM, there are no backbone dihedrals defined and all beads have a mass of 72 AMU (in Martini SC beads have a lower mass).

Elnedyn is probably most used.

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