Dear Gromacs Users!<br><br><br>I want to perform simulation of the pure bilayer surrounded by water. I'm using already pre-equilibrated bilayers as the initial structure. During conversion pdb-> gro -> pdb the velocities from initial equilibration runs of the structure were lost. Should I start generating this velocities in my production run ( gen_Vel= yes) or i must do equilibration instead first to generate velocities? Finally what length should this equilibration be to provide reasonable velocities for futrher MD run if I would avoild long equilibration period because of suitability of my initial model?<br>
<br><br>Thanks for help,<br><br><br>James<br>