GROMACS version: 2023
GROMACS modification: No
Hi everyone, I am trying to do free energy perturbation for nucleotide mutation. I have generated the hybrid topology from pmx and used the MDP files shared in the tutorial by Justin Lemkul for running the FEP. However, the system blowed up with LINCS error after lambda = 12. It seems that tutorial MDP file is not working with DNA molecule and some changes need to be made.
Can anyone share a sample MDP files to be used for purturbing the DNA?
I am doing FEP for first time.