Dear Gromacs users, -The usual target is: hopefully exploring different areas of the phase space by running at least three independent MD experiments starting with three different velocities
-The usual scenario is: (Minimization) then (equilibration) then (production) I generate velocities at the beginning of the equilibration (gen_vel is set to yes, and gen_seed is set to -1 in the equlibration .mdp) and continue to the production (gen_vel is set to no in the production .mdp). -The assumption is: By running a new equilibration for each MD experiment, I guarantee ending up having different statrting velocities for the production phases of these independent experiment and achieve the above target. The confusing part for me here is that the protein is position-restrained during the equlibration and only the solution is allowed to equilibrate using the assigned velocities. -Is the above assumption right? If yes, is there a better way? If no, how could I achieve the above target? -Does the protein atoms get assigned velocities at the start of the equlibration (different velocities by running the equlibration again) and not allowed to use it until the are released from the position-restrain at the beginning of the production? I would appreciate any help responding to the above questions and thoughts. Hassan
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