Typo in the manual (stochastic dynamic)?

User discussions
1

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

2

In the code the factor inside the square root is (1-(exp(-gamma*dt))^2), which looks correct to me. So the manual should be corrected.

3

Hi Berk,

the problem is not the definition of the factor alpha=1-exp(-gamma dt), that is correct, but the update on velocities. The factor inside the square root should be alpha*(2-alpha), not (1-alpha^2).

4

Yes, we are both talking about the same issue in the velocity update. The correct formula I wrote in my reply and that is in the code is mathematically identical to the one of Goga et al.

5

Ah, ok I see now. Alright, then it’s just a documentation problem.