Dear prof. Venable and Nilsson,
thank you for your answers. I am using both files as they are, but I just wanted to check.
Also, regarding the Langevin thermostat/dynamics. Since in the examples and recommended scripts in the documentation there is only one file for heating, equilibration and analysis runs, I was just wondering where is the limit of each phase? After certain amount of time, am I supposed to switch to normal dynamics or proceed with LD?
Do you have some suggestions on how to properly equilibrate system with RNA?