[gmx-users] Bonded parameters from all atom to CG

[Steven Neumann]

Dear Gmx Users,

I run a simulation of trimer (ALA, ALA, ALA) in TIP3P water model
using 298 K at pressure of 1 bar. I am trying to build coarse grained
model. I know how can I get non bonded parametrs (LJ) but I am
confused about bonded parametrs.

Whether I will translate my xtc trajectory to dcd, topology from gmx
to psf file and use VMD plugin "Extract Bond/angle Params from AA Sim"
- is that a good approach? I mean - is the Boltzmann inversion a
proper technique for Coarse Grained simulations or would you suggest
something else?

Steven