GROMACS version: 2023
GROMACS modification: Yes/No
Hi everyone,
I have done the MD simulation of the protein-peptide system using the charmm36 force field. After that, I tried calculating the binding free energy between protein and peptide using gmx_MMPBSA and plotted the graph between delta G and frame #. In the plot, the value of delta G is 0 at some frame. What does that indicate? I have applied the PBC on the trajectory but still getting the same results.
Any comments or suggestions regarding this will be highly appreciated.
I really appreciate any help you can provide.
As I just replied in another thread, G_mmpbsa analysis - #2 by MagnusL, there are not many gmx_mmpbsa experts here.
I haven’t used the gmx_mmpbsa tool at all myself, but in general, when you analyse delta G you always need to know what you are comparing to. If not having a specific reference state, it is common to set the lowest delta G to 0. You could then consider delta G to be delta delta G relative to the most favourable configuration. However, if many frames have exactly delta G 0, that is suspicious.
Thank you for the reply.
I have used starting structure as a reference, so if delta G is zero it means w.r.t reference there is no difference is binding at that particular frame.