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After each cycle, a set of structural coordinates was saved for energy minimization.
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Until vehicle remains in the scene, its coordinates are saved, and as the vehicle leaves the scene, the buffer defined above is updated, and the vanishing flag value is set to 1 representing vehicle exit the scene.
Both of the cutoff distances for long-range electrostatic and van der Waals interactions were set to 10.0 Å, time step was set to 2 fs in all of the simulations, coordinates were saved every 1 ps to record the molecular dynamics trajectory.
Coordinates were saved every 4.8 ps.
Time step used was 2 fs and the coordinates were saved every 10 ps for analysis.
Coordinates were saved every 500 simulation steps producing 5000 frames per run.
All the simulations were performed with a time step of 1fs, and the coordinates were saved every 1ps.
Coordinates were saved every 0.2 ps, and SHAKE was used to hold hydrogen bond lengths near their equilibrium values [55].
Hydrogen atoms were added using standard topological rules in Sybyl v.8.0 [92] and coordinates were saved in mol2 format.
The coordinates were saved every five picoseconds and the analysis was performed using GROMACS v.3.2.1 simulation package [29].
Associated with each pixel vector, the corresponding image coordinates were saved for a later reconstruction of the compositional images.
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