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An initial minimization step was performed for 6000 steps, followed by 20 ns of relaxation.

This minimization step was followed by heating phase (nPT) where the system was brought from 5 to 300 K over 100 ps, followed by 400 ps of equilibration at 300 K. Equilibration was followed by a 100 ns production run, except for the simulations of Sp20, Sp23, Sp24 and Sp25, in which production was performed for 500 ns.

Then the complexity of each minimization step is (O |B|^2)+O k|B|)), and the number of steps required is assumed to depend only on |B|.

In this step the binary files for the energy minimization step are prepared.

In particular, the time taken per alternating minimization step is O ((n n z (P ) + N g f g + N d f d ) k 2 T ), where nnz(P) denotes the number of non-zeros in P, and T is a small constant.

The energy difference of 0.05 Kcal/mol between two successive structures during both minimization steps was used as the termination criterion.

Thus, GGA3 SAR1 protein protein interaction was modeled using the template protein complex and a subsequent energy-minimization step was pursued using GROMACS (Version 4.5.5) 57 to achieve a stable form of the modeled complex.

Minimization: protein solvation and minimization steps were performed using the Molecular Modeling ToolKit (MMTK) (15).

Both pre- and post-process minimization steps were set as 100 and 50, respectively.

For each window, 10 000 energy minimization steps were carried out using a steepest descent algorithm.

A sequence of energy minimization steps were performed as described by Alanazi et al. [ 31] on native and mutant protein structures by using InsightII/Discover (Accelrys Inc., San Diego, CA).