Hi!
I am following the tutorial
http://www.mdtutorials.com/gmx/free_energy/08_advanced.html
Free Energy Calculations: Methane in Water
In the sample MDP files, the simulation time is very small for the production runs. I assume it is due to the small size of methane and it requires little time to reach equilibrium. Is it right? In other words, for larger molecules, do I need longer time? How do I know if the time is enough (By checking system energy, etc.) ?
Also, in the advanced applications page, it mentions constraining the orientation of ligands. Do I just do the regular way to fix the molecule (#include posres.itp)? Do I need to restraint both protein and ligands?
Thank you very much!