When defining the box dimention then how do I know about the distance of protein from the box wall? Which should be greater than half of the Cut-Off (1.4nm) (according to some tutorial).
Then what are longest cutoff which must be shorter than half the shortest box vector to satisfy the minimum image convention. I am asking because I have run gromacs from default parameter of some other tutorial. I have used 0.75 value for -d when using editconf. -- Pawan
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