Gromacs Solvant Box : Biochemistry


Gromacs Alogrithm help.

What I have: We have unit water boxes spc, tp etc. They have opposite sides complementary to each other (please correct me) such that if stacked together we get a uniform water box. “solvate” method creates a bigger box from unit boxes.

What I did I am trying to create a water box without gromacs, using my own code. Need to use same calculations. I tried spc216, the smallest axis is 1.916 nm and did 5x4x5 boxes. I tried 1.916 value for linear transformation in all axis but it still gives a sort of visible gap between adjacent boxes. Tried different values like 1.87, 1.90 but not sure which value will create uniform box.

Question: How does gromacs stack the unit water boxes?

How does it calculates the extension/gap/addition/multiplication values to extend box in all axis? What is this algorithm/calculations/formula?


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