GROMACS version: 2021.4
GROMACS modification: No
To observe the spontaneous binding of a small molecule to a protein, I simulated a system containing 100 copies of the small molecule and the protein.
During the simulation, the index of the molecule spontaneously bound to the active site of the protein was checked, and I measured the nonboned interaction energy (LJ-SR, Coul-SR) between it and the protein using gmx energy (after rerun).
However, the energy between the selected molecule and protein was zero for the entire simulation time.
It seems that the nonbonded interaction energies between each of the 100 copies of the molecule and the protein are summed up for the small molecule with the first index.
I want to measure the change in the nonbonded interaction energy during the binding process of the selected molecule and protein.
please help me
Thanks
It is more likely that you computed the interaction energies while running mdrun on a GPU, which does not support this feature. Make sure you are computing interaction energies only on CPU hardware.
I set energygrps in the mdp file and measured the energy after rerun with -nb cpu.
Energy measurement works well when one ligand is present in the system.
However, in this case, there seems to be a problem because there are 100 identical ligands.
energygrps = protein molecule001
In this case, the nonbonded interaction energy value is equal to the sum of all energy values between 100 molecules and proteins.
energygrps = protein molecule002
energygrps = protein molecule003
.
.
.
energygrps = protein molecule100
In each of these cases, the energy value is measured to be 0.
I want to measure the nonbonded interaction energy between a specific molecule out of 100 and the protein.
You need to create separate index group for the molecule you need and rerun the trajectories with new index name in energygrps.
I already created an index for a specific one out of 100 molecules and measured the energy for it.