# Reproducing the mdp file parameter settings of the NPzAxyT ensemble synthesis

**URL:** <https://gromacs.bioexcel.eu/t/reproducing-the-mdp-file-parameter-settings-of-the-npzaxyt-ensemble-synthesis/10433>\
**Category:** User discussions\
**Tags:** mdp-parameters\
**Created:** [October 29, 2024, 6:39am UTC](https://gromacs.bioexcel.eu/t/reproducing-the-mdp-file-parameter-settings-of-the-npzaxyt-ensemble-synthesis/10433 "2024-10-29T06:39:26Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Yolo-kk](https://avatars.discourse-cdn.com/v4/letter/y/9dc877/32.png) [@Yolo-kk](https://gromacs.bioexcel.eu/u/Yolo-kk)\
**Post date:** [October 29, 2024, 6:39am UTC](https://gromacs.bioexcel.eu/t/reproducing-the-mdp-file-parameter-settings-of-the-npzaxyt-ensemble-synthesis/10433/1 "2024-10-29T06:39:26Z")

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GROMACS version:2022.6  
GROMACS modification: Yes/No  
I have a quick and naive how-to question as a new user. I would like to work on the simulation as the literature describes. The mdp file settings for my equilibration simulation section and the Production Simulation section that follows are as follows. However, the results after the simulation are not the same as expected, and I’m curious if one of the parameters in the mdp file is not set correctly.(The mdp files for Equ and Production sections are attached)

The description in the REF is as follows: the system underwent equilibration in the _NPzAxyT_ ensemble to achieve equilibrium at 1 bar. In this ensemble, _Axy_ indicates fixed box In this ensemble, Axy indicates fixed box dimensions in the _xy_ directions, while _Pz_ denotes the controlled pressure in the _z_ direction. The production run adopted the _NPzAxyT_ ensemble with a Nose-Hoover thermostat at 1 bar. The production run adopted the NPzAxyT ensemble with a Nose -Hoover thermostat at 298 K and a Parrinello-Rahman barostat at 1 bar. Long-range electrostatic interactions were computed Long-range electrostatic interactions were computed using a particle mesh Ewald algorithm with an interpolation order of 4 and a grid size of 0.12 nm. Short-range cutoff distances for van der Waals and Coulombic interactions in direct space were set to 1.2 nm. Integration of the Newtonian equation of motion employed a leapfrog integrator with a time step of 2 fs over a 50 nm time step. Integration of the Newtonian equation of motion employed a leapfrog integrator with a time step of 2 fs over a 50 ns trajectory.

Thanks！！！  
[Equ.mdp](https://gromacs.bioexcel.eu/uploads/short-url/RZLhyK3bvh5WubE8GQiumxTP6n.mdp) (2.5 KB)  
[Production-Sim.mdp](https://gromacs.bioexcel.eu/uploads/short-url/76jOtjb4cRiLgk03vEvuxYYCHeR.mdp) (2.4 KB)

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [October 29, 2024, 7:54am UTC](https://gromacs.bioexcel.eu/t/reproducing-the-mdp-file-parameter-settings-of-the-npzaxyt-ensemble-synthesis/10433/2 "2024-10-29T07:54:32Z")

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Hi,  
If you are uncertain about your settings you should be able to ask the authors of the manuscript for theirs (which may only be directly applicable if they were also using GROMACS). But a quick glance shows a few things you should consider changing to:

```auto
tau_p = 5.0 ; Time constant for coupling (ps)
compressibility = 0 4.5e-5 ; Compressibility in xy and z

```

They say that they used an ensemble with fixed box dimensions in xy directions. They did not specify tau-p, but 5 to 10 ps is usually good with `parrinello-rahman`.

They say that they used a Nose-Hoover thermostat (in the production run), whereas you are using a velocity-rescale thermostat in the equilibration run (they don’t say anything about the equilibration thermostat). Personally, I think your choice is better, but may not be exactly according to their settings. I would recommend a `tau-t` of 2 ps (instead of 0.5).

In the end, I think it’s mainly the `compressibility` setting that makes the difference.

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**Author:** ![Yolo-kk](https://avatars.discourse-cdn.com/v4/letter/y/9dc877/32.png) [@Yolo-kk](https://gromacs.bioexcel.eu/u/Yolo-kk)\
**Post date:** [October 29, 2024, 8:31am UTC](https://gromacs.bioexcel.eu/t/reproducing-the-mdp-file-parameter-settings-of-the-npzaxyt-ensemble-synthesis/10433/3 "2024-10-29T08:31:44Z")

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I really appreciate the time and effort you took to respond to my question. Your answer provided valuable insights and was incredibly helpful for guiding my work. It has definitely clarified a lot of the issues I was facing.