# Free Energy Perturbation with Leap Frog

**URL:** <https://gromacs.bioexcel.eu/t/free-energy-perturbation-with-leap-frog/4481>\
**Category:** User discussions\
**Created:** [July 20, 2022, 3:41pm UTC](https://gromacs.bioexcel.eu/t/free-energy-perturbation-with-leap-frog/4481 "2022-07-20T15:41:18Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![hij09373](https://avatars.discourse-cdn.com/v4/letter/h/b38774/32.png) [@hij09373](https://gromacs.bioexcel.eu/u/hij09373)\
**Post date:** [July 20, 2022, 3:41pm UTC](https://gromacs.bioexcel.eu/t/free-energy-perturbation-with-leap-frog/4481/1 "2022-07-20T15:41:18Z")

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GROMACS version: 2022-rc1  
GROMACS modification:No

Hi, I am a quite new user of Gromacs, and I have a basic question related to the integrator for Free Energy Perturbation calculation as written in the tutorial of Justin Lemkul. In the tutorial, the integrator is set as stochastic dynamic. Nevertheless, I want to know what happened if I run my FEP with Leap Frog. So I run the vdW-coupling process applying Gauss Legendre Quadrature nodes, I got a note from Gromacs:

“NOTE 1 [file /home3/hij09373/fep/2\_ribo\_water/MDP\_vdw/nvt\_0.mdp, line 81]:  
For proper sampling of the (nearly) decoupled state, stochastic dynamics  
should be used”

So I assume, that Leap Frog is not preferable in this case, at least for nearly decoupled states. Due to my background in quantum chemistry and not MD, I am not quite sure what is the impact of “decoupled state” with either LF oder Langevin. While I do might understand the difference between the integrators, I might miss some crucial points in these detailed aspects in FEP. May be somebody has already answered this, but at the moment I could not find this. Can somebody explain this in short or even give me some elaborate literatures?

Many thanks

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [July 28, 2022, 12:20pm UTC](https://gromacs.bioexcel.eu/t/free-energy-perturbation-with-leap-frog/4481/2 "2022-07-28T12:20:36Z")

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Decoupled atoms/molecules are not coupled to the rest of the system and can therefore have incorrect velocity distributions. The SD integrator guarantees correct velocity distributions for all degrees of freedom.