Reproducing the mdp file parameter settings of the NPzAxyT ensemble synthesis

User discussions
1

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 (2.5 KB)
Production-Sim.mdp (2.4 KB)

2

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:

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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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.