To obtain high-intensity electromagnetic field (high compared to the inner-atom field) and not to destroy the sample, one can use methods of the local field enhancement.
Multiple short simulations were performed, at least 3 × 20 ns, for each peptide at 25°C using our in-house MD package in lucem molecular mechanics (ilmm) (Beck et al., 2000 2014), with the Levitt et al. (1995) all atom force field and the F3C water model (Levitt et al., 1997).
The structure was solvated with water inside a cubic box with a length of 7.5 nm, and minimised and equilibrated for 0.1 ns (NPT and NVT, respectively), with positions restraint on all heavy atoms followed by five unrestrained simulations of about 100 ns with explicit solvent employing OPLS all-atom force field and the TIP3P water model [47,48].
The potential energy is calculated with all-atom force field and implicit solvent model (GB/SA) [25], [26].
The second scoring module first minimizes the model with MMTSB [36] and CHARMM [37] using the PARAM22 [38] all-atom force field and a distance-scaled electrostatic potential with a dielectric constant equal to 4 [39].
We calculated the contact energies by all-atom force field and found that the residues with lowest contact energies (or strong inter-residue interactions) are in good agreement with the structurally conserved residues identified previously.
For simulation, we used the CHARMM program with the param27 all-atom force field and additional parameters for Hyp.
It is based on the CHARMM package, and uses an all atom force-field and rotamer libraries to describe and evaluate side-chain types and conformations.
By numerically solving the coupled Bloch Maxwell equations for atom and field simultaneously in space and time, we demonstrate dynamic control of light propagation and optical switching in such a four-level atomic medium.
That reverses the polarity of the atom's magnetic field and ejects it from the trap.
The docked protein-ligand complex and ligand were then submitted to multi-scale Truncated Newton energy minimization in all-atom OPLS force field and Generalized Born (GB) solvent using the Protein Local Optimization Program (PLOP) [50], [51], [52].
