The velocity verlet integrator was used with an integration step of 2 fsec.
One should either delay the pulse by one integration step (DT or DTMAX depending upon the integrator), or set the start time to be before the first dose by at least one integrator time step.
Only our model has two nearly pure integration steps: the tVOR integrator is a pure integrator and the velocity-to-position neural integrator has the usual time constant of 20 seconds, and thus this model best maintains eye velocity during sustained translation.
The solvated system was subjected to energy minimization to remove the steric conflicts between atoms of protein and water molecules having a maximum step of 2000 with steepest descent integrator, that converge the energy when the maximum force was smaller than 1000 kJ·mol−1·nm−1.
Subsequently, a 100000-step simulated annealing protocol with an integrator time step of 1 fs was performed.
Paige and colleagues [39], [40] included two integration steps, the common velocity-to-position neural integrator, and a second, leaky tVOR integrator (time constant 250 ms) in series with a high-pass filter (time constant 50 ms).
Determine the maximum step size: (9).
In version 8.3.18, the pulse has been redefined to be delayed by one integrator time step.
First, a 1000-step energy minimization was performed with an iteration time of 1 fs without experimental restraints, followed by a 100000-iteration simulated annealing protocol with an integrator time step of 1 fs.
These last two steps are iterated until convergence or a maximum number of steps is reached.
