Free Energy Calculations

User discussions
1

GROMACS version:2024.4
GROMACS modification: No

Hello all,

I have run two simulations (using same forcefieds and .mdp files) with a protein- small peptide system and I want to compare the free energies of the peptides to see which one has a higher stability throughout the trajectory. Unfortunately I am very new to gromacs and do not know how to extract these free energies from the trajectories. I was trying gmx energy, but I realized I did not put in the peptide as a group in the .edr.

Here is my .mdp file:
integrator = md
nsteps = 500000000 ; 2 * 500000000 = 1000000 ps (1000 ns)
dt = 0.002 ; 2 fs
; Output control
nstenergy = 5000
nstlog = 5000
nstxout-compressed = 5000
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = h-bonds
lincs_iter = 1
lincs_order = 4
; Neighbor searching and vdW
cutoff-scheme = Verlet
ns_type = grid
nstlist = 20
rlist = 1.2
vdwtype = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2
; Electrostatics
coulombtype = PME
rcoulomb = 1.2
pme_order = 4
fourierspacing = 0.16
; Temperature coupling
tcoupl = V-rescale
tc-grps = Protein_TYF Water_and_ions
tau_t = 0.1 0.1
ref_t = 298 298
; Pressure coupling
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
; Periodic boundary conditions
pbc = xyz ; 3-D PBC

DispCorr = no
; Velocity generation
gen_vel = no

It would be very helpful if I could get the free energies.

Thank you so much for your time.

2

The short answer is: you don’t. You can’t obtain a free energy directly from an MD simulation. There may be post-processing (e.g. MM/PBSA) but accuracy may vary. If you want a binding free energy, you have to do a robust series of calculations (umbrella sampling, alchemical transformation, etc) to obtain it.