[gmx-users] Simulation of the pure lipid bilayer

[James Starlight]

Dear Gromacs Users!


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?


Thanks for help,


James
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