GROMACS version: 2023.1
GROMACS modification: No
Hello,
I assume that it’s a simple question, but how exactly do we define the Initial energy value to be used in PMF diagrams, during a steered MD of a drug molecule from the centre of a bilayer symmetrical system to the water part of the system?
Thank you for your time
Hi @EOrfanakis
Energies in general have little meaning when they are taken as absolute values. The important quantity is how much do they change in two different states, e.g., within the bilayer and outside it. It is usually set to zero where it has its lowest value (the global minimum of the PMF).
Thank you for the reply.
I try to reproduce US of 12 compounds referred in this paper: A Method to Predict Blood-Brain Barrier Permeability of Drug-Like Compounds Using Molecular Dynamics Simulations
As you may see, in this paper at FIGURE 3 (B), i am wondering about the initial energy value at the PMF diagram.