# Free Energy Calculation **URL:** \ **Category:** User discussions\ **Created:** [September 1, 2020, 8:45am UTC](https://gromacs.bioexcel.eu/t/free-energy-calculation/746 "2020-09-01T08:45:40Z")\ **Posts on this page:** 4\ **Page:** 1
**Author:** ![vg87](https://avatars.discourse-cdn.com/v4/letter/v/65b543/32.png) [@vg87](https://gromacs.bioexcel.eu/u/vg87)\ **Post date:** [September 1, 2020, 8:45am UTC](https://gromacs.bioexcel.eu/t/free-energy-calculation/746/1 "2020-09-01T08:45:41Z")
GROMACS version: 5.1.4 GROMACS modification: No Hi all, I have run a free-energy perturbation (FEP) with the **slow-growth approach**. So, my lambda increases at each MD step till reaching the value of 1 at the last step of my MD. So, for each step, I get force on a given lambda values. Do you know how to integrate it along the lambda growth to get the free energy? gmx bar does not be able to handle such a structured xvg file. I think it expects a constant lambda value and different xvg files instead. Considering I am also running reverse alchemical transformation. Thanks everybody for your contribution. Cheers VG ---
**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\ **Post date:** [September 4, 2020, 12:06pm UTC](https://gromacs.bioexcel.eu/t/free-energy-calculation/746/2 "2020-09-04T12:06:58Z")
Hi vg87, Slightly indirect answer - if you can do slow-growth in both ways, you can also do fast-growth and that will be more robust in almost all cases. For a neat set of tools to analyse that type of data see [http://pmx.mpibpc.mpg.de/](http://pmx.mpibpc.mpg.de/) You can even use some of the analysis scripts there to integrate your slow-growth data. ---
**Author:** ![vg87](https://avatars.discourse-cdn.com/v4/letter/v/65b543/32.png) [@vg87](https://gromacs.bioexcel.eu/u/vg87)\ **Post date:** [September 30, 2020, 7:53pm UTC](https://gromacs.bioexcel.eu/t/free-energy-calculation/746/3 "2020-09-30T19:53:39Z")
Thanks a lot! I will make a try! V ---
**Author:** ![vg87](https://avatars.discourse-cdn.com/v4/letter/v/65b543/32.png) [@vg87](https://gromacs.bioexcel.eu/u/vg87)\ **Post date:** [September 30, 2020, 8:03pm UTC](https://gromacs.bioexcel.eu/t/free-energy-calculation/746/4 "2020-09-30T20:03:43Z")
Actually what I have done so far: I am transforming one of the non-bridging oxigen of a phosphate group in a TA dinucleotide into an S. So I am passing from Rp to Sp stereochemistry and asses the difference in terms of energetics. Here the ‘free-energy’ setting I have intensely discussed with Justin Lemkul along these days: == SETTING == ; Free energy control stuff free\_energy = yes init\_lambda\_state = 0 delta\_lambda = 0 calc\_lambda\_neighbors = 1 ; only immediate neighboring windows couple-intramol = yes ; init\_lambda\_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 vdw\_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 coul\_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 bonded\_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 mass\_lambdas = 0.00 0.10 0.20 0.30 0.40 0.50 0.60 0.70 0.80 0.90 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 ; init\_lambda\_state 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 restraint\_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 ; Options for the decoupling sc-alpha = 0.5 sc-coul = no ; linear interpolation of Coulomb (none in this case) sc-power = 1 sc-sigma = 0.3 nstdhdl = 10 while here the results: point 0 - 1, DG 6.36 +/- 0.04 point 1 - 2, DG 4.99 +/- 0.07 point 2 - 3, DG 3.48 +/- 0.04 point 3 - 4, DG 2.72 +/- 0.05 point 4 - 5, DG 1.87 +/- 0.04 point 5 - 6, DG 2.33 +/- 0.06 point 6 - 7, DG 1.67 +/- 0.06 point 7 - 8, DG 0.86 +/- 0.03 point 8 - 9, DG 0.09 +/- 0.08 point 9 - 10, DG -0.81 +/- 0.03 point 10 - 11, DG 1.82 +/- 0.01 point 11 - 12, DG 1.54 +/- 0.02 point 12 - 13, DG 1.29 +/- 0.01 point 13 - 14, DG 1.04 +/- 0.01 point 14 - 15, DG 0.75 +/- 0.01 point 15 - 16, DG 0.40 +/- 0.07 point 16 - 17, DG 0.10 +/- 0.08 point 17 - 18, DG -0.11 +/- 0.01 point 18 - 19, DG -0.38 +/- 0.01 point 19 - 20, DG -0.70 +/- 0.03 **total 0 - 20, DG 29.30 +/- 0.30** Now, experimentally I know that passing from a phosphate group (in TA) to a phosphorothioate group (of course in TA) has a dG = +2.5 kcal mol As you may note, values are really really far. Each window is 2 ns long, but even with 5 ns thing do not change. Have you got any idea guys? Thanks in advance for any kind contribution. Regards VG