How do we can determine the shape and size of simulation box in GROMACS that suites best for the target protein?
Does the wrong box shape will have effect on final results of a simulation?
To simulate something in the water we needed at least three-layered shell of water molecules (8 A). Many of the properties will be accurately modeled in the shells of 13-15 A. However, protein +15 A on each side... is a very large model.
A simple answer would be to use a box shape that accumulates less water molecules at the corners for example truncated octahedron, unless you are doing something special with your md simulation. Choosing a box with fewer water molecules will be less computationally expensive and your simulations will run faster.
GROMACS offers a variety of box types: the standard cubical/rectangular box, the truncated octahedron, the hexagonal prism, and the rhombic dodecahedron. Shape of the box can affect the simulation. A box type that best reflects the geometry of the solute/protein should be used. For example, the truncated octahedron approximates a sphere, so it is the optimal choice for globular proteins and other roughly spherical molecules.
you can view shape and size of solvent box surrounding the whole protein using visualization programs like chimera or VMD..
YES, wrong box shape has impact on the results...
To simulate something in the water we needed at least three-layered shell of water molecules (8 A). Many of the properties will be accurately modeled in the shells of 13-15 A. However, protein +15 A on each side... is a very large model.
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