GROMACS version: 2022

GROMACS modification: Yes/No

Hi,

I believe there is a typo in the user manual.

I will be referring to the latest version of GROMACS 2022 Manual | Zenodo.

In section 5.4.7, equation 5.94 (algorithm for stochastic dynamics), the multiplicative factor inside the square root is (1-alpha^2), while in really it should be alpha*(2-alpha), at least according to the paper by Goga et al. that is cited as reference for that formula.

Am I right or am I missing something? When trying to simulate that set of equations with the formula on Goga et al. and the one in the manual I get completely different results, but I get the correct overdamped limit only with the formula by Goga et al.

I hope it’s just an error in the manual, while stochastic dynamics is implemented correctly in GROMACS.

Michele