Data and Software Availability for the manuscript: "Influence of the water model on the structure and interactions of the GPR40 protein with the lipid membrane and the solvent. In silico analysis using nonpolarizable rigid and flexible water models"
Steps to reproduce
1. To run the simulations, you have to compile the system. For example, for the system with the spc/e water model, the following instructions are used: gmx grompp -f md-memb.mdp -c npt-1ns.gro -p topol-G40spce.top -n index-G40spce.ndx -o G40spce.tpr gmx mdrun -deffnm G40spce The files are in the MD-Files folder 2. The VMD or UCSF Chimera programs can be used to visualize the structures. The files are in the Structures, b-Factor, and Electrostatic-Potential folders. 3. To view the graphs of stability indicators, it is recommended to use the XmGrace program. 4. The free energy landscape (FEL) analyses are already built and can be visualized with the Mathematica program in versions higher than 10. 5. Versions of the trajectories obtained in the MD simulations with a step size of 5 ns have been added for the purposes of verifying results. The files are located in the Trajectories folder. The program used was Gromacs 2021.