Calculating vdW and ES energy between molecules

User discussions
1

GROMACS version: 2020.2
GROMACS modification: No

Hello friends,

I wanted to calculate the vdW and ES energy between two molecular groups in my system. However, I have only been successful in calculating vdW and ES energy of the whole system. To calculate the energies between the molecular groups, would I have to make an index file for the 2 molecular groups and use this folder as an input for the gmx energy command or is there something else I should approach? Please let me know any help is appreciated.

Best regards,
Rosa

2

If you want interaction energy between groups, that is what energygrps in the .mdp file is for. Generate a new .tpr file with the desired groups, and use mdrun -rerun to recalculate the energies from the existing trajectory.

3

Dear Justin,

Thank you for your reply. I have successfully calculated the interactions energies between two molecular groups.

Best regards,
Rosa