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Table 1 A schematic sketch of molecular dynamics procedure

From: Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant

Step Constrain/Algorithm Temperature Pressure Time Neighborsearching Electrostatic interactions (long-range) Temperature coupling Pressure coupling
Geometry Optimization No - - 2 ns grid Particle Mesh Ewald (PME) - -
Temperature constant No 300 K - 0.1 ns grid PME V-rescale -
Pressure constant No - 1 bar 0.1 ns grid PME - Parrinello-Rahman
Total molecular dynamics Yes/steep = steepest descent minimization 300 K 1 bar 10 ns grid PME V-rescale Parrinello-Rahman