GROMACS version: 2020.3
I am calculating free energy perturbation (FEP) for converting state A to state B and vice versa using the following for the free energy variables in the mdp file:
free-energy = yes
init-lambda = 0 (and 1 for B state)
delta-lambda = 1e-5 (and -1e-5 for B state)
sc-alpha = 0.3
sc-sigma = 0.25
sc-power = 1
couple-lambda0 = vdw-q
couple-lambda1 = none
couple-intramol = yes
nstcalcenergy = 1
nstdhdl = 1
It seems that the equilibration and transition runs go well, but I have problems with analyzing the results.
My question is if it’s possible to use “gmx bar” to analyze such a system? And if not, what are the alternatives?