GROMACS version: 2021.3
GROMACS modification: No
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I am studying adsorption of micelles on a surface using MARTINI FF. To have a better picture of the groups interacting with the surface, I would like to calculate the interaction energy of different CG beads with the CG surface.
I have the following questions:
- Is interaction energy obtained using MARTINI FF relevant? According to Justin’s tutorial on protein, only CHARMM is suitable. But I guess there he compared commonly used AA/UA FFs and was wondering if MARTINI is suitable as the beads are pareterized based on thermodynamic parameters.
- The system has many micelles and unimers but only 1-2 micelles are interacting with the surface. Even the micelle which interacts with the surface, there is considerable dynamic behaviour within the micelle itself (some molecules interact with surface, then desorb and other molecules adsorb - this is expected because the molecules within a micelle will compete to bind to the surface). In such a situation, how can I study the interaction energy of different beads in a molecule (each molecule has >25 beads, each micelle has about 20 such molecules and the entire system has >100 such molecules)?