GROMACS version: 2022.2
GROMACS modification: No
Hello, everyone!
I need to evaluate the free energy contribution of maintaining a molecule within a fixed distance from the center of mass of a phase. I did this by using the umbrella pull code. However, since I only use a single window, I can’t realy use WHAM.
The idea is to calculate the free energy difference between the state where there’s no pull and with the pull code on.
Does anyone know how I could do this?
If I understand you correctly, you can’t get the free energy difference from the data you’ve got. You can get the force that is applied to keep the molecule in place, from the pullf.xvg file. That doesn’t give you the free energy, though.
Sure, but is there a way I could couple the pull code with a free energy calculation (maybe with a lambda) to evaluate this free energy difference?
It should work with the free-energy options. See Molecular dynamics parameters (.mdp options) - GROMACS 2024.2 documentation and Molecular dynamics parameters (.mdp options) - GROMACS 2024.2 documentation.
Then you can analyse it using gmx bar.