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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