# Typo in the manual (stochastic dynamic)?

**URL:** <https://gromacs.bioexcel.eu/t/typo-in-the-manual-stochastic-dynamic/3867>\
**Category:** User discussions\
**Tags:** documentation\
**Created:** [March 21, 2022, 4:03pm UTC](https://gromacs.bioexcel.eu/t/typo-in-the-manual-stochastic-dynamic/3867 "2022-03-21T16:03:24Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [March 21, 2022, 4:03pm UTC](https://gromacs.bioexcel.eu/t/typo-in-the-manual-stochastic-dynamic/3867/1 "2022-03-21T16:03:24Z")

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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](https://doi.org/10.5281/zenodo.6103568).  
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

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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:** [March 25, 2022, 12:00pm UTC](https://gromacs.bioexcel.eu/t/typo-in-the-manual-stochastic-dynamic/3867/2 "2022-03-25T12:00:13Z")

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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.

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [March 28, 2022, 8:26am UTC](https://gromacs.bioexcel.eu/t/typo-in-the-manual-stochastic-dynamic/3867/3 "2022-03-28T08:26:06Z")

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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).

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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:** [March 28, 2022, 9:07am UTC](https://gromacs.bioexcel.eu/t/typo-in-the-manual-stochastic-dynamic/3867/4 "2022-03-28T09:07:55Z")

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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.

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**Author:** ![MichelePellegrino](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/michelepellegrino/32/628_2.png) [@MichelePellegrino](https://gromacs.bioexcel.eu/u/MichelePellegrino)\
**Post date:** [March 28, 2022, 9:27am UTC](https://gromacs.bioexcel.eu/t/typo-in-the-manual-stochastic-dynamic/3867/5 "2022-03-28T09:27:10Z")

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