using user-colvars to calculate PMF

Hi dear LAMMPS users,

Recently, I try to use user-colvars to compute PMF. In my simulation, I want to compute the free energy change when one molecule(x) desorpt from the surface. As shown in the diagram below, my simulation box is an equilibration state of many molecules adsorption on the surface. The surface stay static during the simulation through setforce zero and without displacement&velocity integration. x(as you can see in the diagram) upon the surface are adsorptive molecules. And the xyz are all periodic boundary conditions.

Diagram 1:

Hello Shusen, based on your setup, ABF (but really any other free energy calculation method) will only be sensitive to the internal forces of atoms 2-6, but not those of the surface that you froze. This will be accurate only for as long as the surface wouldn’t move otherwise, i.e. there is no work done on it.

I strongly recommend that you try to understand your problem first, preferably discussing with your advisor and worrying about how to implement the calculation as a second stage.

I do not recommend picking an example from another mailing list message that could have very little in common with your problem, especially seeing as you did not even specify what was the system studied in that example.

Giacomo