GROMACS version:2025.4
GROMACS modification: No
Hi I did this tutorial: aminoacid_tutorial which involves calculating the change in folding free energy between a protein and it’s mutant. I wanted to replicate the results, only calculating it with independent replica FEP.
I can’t really find much online detailing what a good protocol is for this. At this moment, I’m taking the system generated from the instructions in the tutorial and I’m minimizing, equilibrating, and running production without the free energy section in the mdp files. Next, I’m creating a number of equilibration and production mdp files for the different lambda windows.
Calculating the free energy change for the unfolded protein was easy and gave good quality results according to all the tests I did with alchemlyb. However, when I try to do the folded protein, it always gives terrible results with bad phase overlap no matter how many lambda windows I add or how long I run each of them for.
I tried to split the singular fep-lambdas setting into it’s different components since I read somewhere that it can improve the results, but it consistently gives me 1000 LINCS WARNINGs when I try to equilibrate for most of the frames.
I’m still very much a novice at this point and I feel as though that I’m doing something fundamentally wrong here. I linked the mdp files that I used to calculate the unfolded below. It should be identical to the framework that I was using for the folded. Any help would be greatly appreciated.
em.mdp (1.1 KB)
fep_l0.mdp (8.3 KB)
eq_l0.mdp (8.3 KB)
prod.mdp (7.4 KB)
eq_nvt.mdp (7.4 KB)
eq_npt.mdp (7.4 KB)