GROMACS version:2021.4-Ubuntu-2021.4-2
GROMACS modification: Yes/No
Hi, I am new to GROMACS… I run a simulation and at the analysis stage I wanted to calculate the Avg distance between an Amide on my ligand and two residues in the protein binding pocket. Surprisingly, traj dump(t=0) looked different from the crystal structure used for the simulation. Specifically, in the crystal structure there were 2 Hbonds between the ligand and residues in the binding pocket that I wanted to track throughout the simulation, however at trj dump (t=0) these Hbonds dont exists and when I calculated the Avg distance between the protein residues and the ligand the “Average distance: 1.12404 nm” which ~10A". How can this happen?
After energy minimization and equilibration, the coordinates change.
Without knowing how you computed the distance (which exact groups), we can’t comment on the analysis, but I doubt that the t=0 frame has a 1.1-nm distance between atoms that had been H-bonded, unless you did not properly restrain the system during equilibration. Perhaps the index groups you used to compute the distance were not appropriate?