Interaction Energy Between Protein and Membrane Environment

User discussions
1

GROMACS version: 2018
GROMACS modification: No
Hello everyone,

I’m interested in measuring the interaction energy between a membrane protein and its environment, both by itself and as a dimer to estimate which is more likely in vivo. I’ve run ~500 ns of Martini simulations, and am hoping that there is a post processing way to parse the energy file, though of course I can rerun these simulations if needed. Happy to read through any documentation or manuscripts, but I was having difficultly finding a place to start and appreciate any assistance!

Best,
Alex

2

Generate a new .tpr file from an .mdp file specifying the desired energygrps, then re-calculate the energies via mdrun -rerun on the existing trajectory. There will be new selections in the resulting .edr file corresponding to the interaction energies. Note that these quantities may not be physically meaningful.