[gmx-users] PROTEIN-LIGAND SIMULATION

[Subashini .K]

Hi gromacs users,


In order to calculate binding energy of single protein inhibitor complex through simulations, how long should we run the calculations?


Is 2ns sufficient?


How to obtain results and plot time (in ps) along x-axis and binding energy (kJ/mol)along y-axis?


Had completed two equilibration phases (NVT and NPT)and then used the command for production MD (for 2ns).


Can someone help?


Thanks,

Subashini.K