Replication Data for: Light Martini water accelerates sampling in coarse-grained molecular dynamics simulations

We systematically reduced the mass of the Martini water beads and verified stable, accurate integration of the equations of motion with 20 fs time steps, as typically used in Martini simulations. Light Martini water has a reduced mass of 20 amu (compared to 72 amu in the standard water model), yielding up to a 2.68-fold increase in the sampling rate of IDP chain reconfiguration in water and a 16 % increase in the lateral diffusion of lipids in a POPC bilayer.

Equilibrium properties remained unaffected by the mass scaling, and the speedup was achieved without compromising simulation accuracy. The water model is trivial to implement, has no computational overhead, and should be universally applicable to Martini simulations. Dataset Description This dataset contains files to reproduce the data presented in the presented in the article "Light Martini water accelerates sampling in coarse-grained molecular dynamics simulations".

The files, mainly in- and output files of MD simulations, are organized as follows, similar to the structure of the article. Trajectories are not included, but available upon reasonable request. The file martini_v3.0.0_solvents_v1.itp contains the Martini 3 solvents force field parameters, with an added molecule type for our "light Martini water" (moleculetype "LW") developed in this project.

To use it, download this file, include it in your topology (.top) file and replace "W" with "LW" in the [ molecules ] section. The directory 01-LightMartiniWater_development contains all files associated with the construction of the "light Martini water". The mdp directory contains GROMACS mdp (MD simulation parameter) files for the simulation runs.

Each W_* directory contains the files for the corresponding water bead mass. The toppar directory within each W_* directory contains the Martini force field files. The files water.top and waterbox.gro within each W_* directory contain the topology file and initial structure of the simulation box, respectively.

The directories em, nvt, npt, nvt2, nvt2-visc, nve_diffusion and nve_short within each W_* directory contain the files for energy minimization, NVT, NpT and second NVT equilibration, NVT simulation for viscosity calculation, NVE runs to extract the self-diffusion coefficient and NVE runs for analysis of energy conservation, respectively. The directory 02a-single_IDPs contains all files associated with the use of "light" and default Martini water in simulations of IDPs.

The subdirectories represent the different IDP simulation systems. In each subdirectory, one directory for the simulations employing default water (W_72) and one for the simulations employing "light Martini water" (W_20) can be found. In each W_72 directory, the fold directory contains files associated with the prediction of the initial IDP structure.

The files with suffixes _CG.pdb, _W.gro, _W_ions.gro are files of the structure after conversion to the coarse-grained representation, adding water to the simulation box and adding ions to the simulation box, respectively. The resulting initial simulation box was also used for the W_20 simulations. The toppar directory within each W_* directory contains the Martini force field files.

In each W_* directory, the mdp directory contains GROMACS mdp (MD simulation parameter) files for the simulation runs. In the directories em, nvt, npt, prod—subdirectories of both W_* directories—the files associated with energy minimisation, NVT and NpT equilibration and production run, respectively, are deposited. The directories 02b-POPC_membrane and 02b-DPPC_CHOL_membrane contain all files associated with the use of "light" and default Martini water in simulations of a POPC and a DPPC/cholesterol membrane, respectively.

The toppar directory within each W_* directory contains the Martini force field files. The step5_charmm2gmx.pdb and system.top files are the initial simulation system structure and topology files, respectively. In each W_* directory, the mdp directory contains GROMACS mdp (MD simulation parameter) files for the simulation runs.

In the directories em, nvt, npt, prod_*—subdirectories of both W_* directories—the files associated with energy minimisation, NVT and NpT equilibration and production runs, respectively, are deposited. The directory Plots-RawData contains the data plotted in the article figures, as comma-separated values (csv) files. Except for the .tpr and .edr files, which are GROMACS binary files, all files are text files.

The .gro and .pdb files store 3D atomic coordinates of the simulation systems, thus it is recommended to open them using a molecular visualization program. Results can be reproduced using GROMACS.