[gmx-users] does gromos force field can explain pi-pi interaction

Dear gmx users, My simulation shows that the aromatic ring of ligand forms stacking pi-pi interaction with the side chain of Phe of receptor during MD simulation. One reviewer of my manuscript questions that such pi-pi interaction can not accurately accounted for by the employed force field.

[gmx-users] Is 2D projection

Dear gmx users, Does the 2D projection plot has something to do with convergence of the trajectory? If so, what kind of shape of plot shows the trajectory is non-converged? Normally, I use RMSD plot to see if the trajectory tends to converge. Now my concern is how to see whether trajectory is co