[gmx-users] Nose-Hoover vs Berendsen vs V-rescale

[Mark Abraham]

Hi,

It's very likely a good idea to get the velocity distribution right, for
the situation you're trying to model. Check out
https://www.livecomsjournal.org/article/5957-best-practices-for-foundations-in-molecular-simulations-article-v1-0
(and the other great LiveComsJ material!)

Mark

On Thu, 12 Mar 2020 at 07:14, Hadi Rahmaninejad <ha.rahmaani at gmail.com>
wrote:

> Hello Gromacs users,
>
> I hope you are well. I am doing a simulation to get the diffusion
> coefficient of some gas molecules in a material structure. After
> minimization and solvation, I run NVT and then NPT to equilibrate the
> system, and then for production again I am running NPT step. My first
> question is that which system (NVT vs NPT) is more suitable for diffusion
> of gas molecule in a solvent? Second, does this point affect my result
> which 'temperature coupling' I am using? I highly appreciate if you can
> help me with this.
>
> Warm regards,
> Hadi
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