The GJ 436 planetary system is an extraordinary system. The Neptune-size planet that orbits the M3 dwarf revealed in the Ly$alpha$ line an extended neutral hydrogen atmosphere. This material fills a comet-like tail that obscures the stellar disc for more than 10 hours after the planetary transit. Here, we carry out a series of 3D radiation hydrodynamic simulations to model the interaction of the stellar wind with the escaping planetary atmosphere. With these models, we seek to reproduce the $sim56%$ absorption found in Ly$alpha$ transits, simultaneously with the lack of absorption in H$alpha$ transit. Varying the stellar wind strength and the EUV stellar luminosity, we search for a set of parameters that best fit the observational data. Based on Ly$alpha$ observations, we found a stellar wind velocity at the position of the planet to be around [250-460] km s$^{-1}$ with a temperature of $[3-4]times10^5$ K. The stellar and planetary mass loss rates are found to be $2times 10^{-15}$ M$_odot$ yr$^{-1}$ and $sim[6-10]times10^9$ g s$^{-1}$, respectively, for a stellar EUV luminosity of $[0.8-1.6]times10^{27}$ erg s$^{-1}$. For the parameters explored in our simulations, none of our models present any significant absorption in the H$alpha$ line in agreement with the observations.
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