GROMACS version: 2023.1
GROMACS modification: No
Hi everyone,
I am performing umbrella sampling simulations to calculate the free energy profile (PMF). After running gmx wham, I get the PMF relative to the lowest free energy point, which is great for determining relative differences. However, I would like to calculate the initial energy (at the starting point of the simulation) and set it as the reference point for my PMF.
Should i use gmx energy command?
Thank you for your time
What is it you want to achieve? The PMF is just a relative free energy difference along the reaction coordinate. You can of course set the zero-point to any arbitrary value and/or you can recalibrate the PMF so that the zero-point is anywhere. What kind of energy would you like to use and why?
I want to set the zero point at the free energy of a molecule as it’s displayed at this picture:
In that example, it seems like they are just setting the free energy in the solvent to 0. I think you can use the gmx wham -zprof0 option to set the 0 point anywhere along the reaction coordinate. If that doesn’t work, you can just write a Python tool to read the xvg file, shift it up or down, and write it back.
thank you very much!
