I am a beginner with MD. So I have got a simple protein solvated in water, with periodic boundary conditions. Now I have run the MD, and in the trajectory I can see that the water molecules are also moving/vibrating alongwith the protein.
Now I am confused on the solvation part. For the water molecules to move, the potential energy of every water molecule needs to be calculated and force calculated from there. Now potential energy of a water molecule includes VdW & Electrostatic forces from surrounding water molecules and possibly the protein.
Is this how potential energy of each water molecule is calculated and forces calculated from that??
Now coming to the protein standpoint. From the documentation its not clear to me how solvation energy in included in MD steps. Do we include solvation energy in the protein energy profile in every time-step using whatever conformation it is in at that time? If yes, I am not clear which method is used to calculate the solvation energy, is it Self consistent Reaction Field or something else?
Can anyone throw some light on this? I will be grateful for your help.
The potential energy of the system is computed according to the energy function of the force field. The force on any atom is the gradient of that energy with respect to coordinates. This is true of anything in an MD simulation.
There is no such energy term. “The energy of a molecule” is not something that any force field is parametrized to produce in any meaningful way. Relative configurational energy differences are often compared against QM and then validated against condensed-phase properties. But “solvation energy” is more of a free energy concept, like hydration free energy, but it is not a force field term in any conventional MM force field.