1. General topics
  3. Martini Philosophy
  5. what is the difference between elastic network model and elnedyn?

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

  • junfeng
  • junfeng's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
11 years 2 months ago #1401 by junfeng
what is the difference between elastic network model and elnedyn? was created 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?

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

More
11 years 2 months ago #1402 by djurre
Replied by djurre on topic what is the difference between elastic network model and elnedyn?
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.

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

  1. General topics
  3. Martini Philosophy
  5. what is the difference between elastic network model and elnedyn?
Time to create page: 0.126 seconds