Dear users, I ran a simulation of a protein in water with rlist = rcoloumb = 1.4nm, rvdw = 1.0nm, with PME and the distance between in the periodic was set to a minimum of 2.0 i.,e distance between protein and cell edge was set to 1.0nm, Even then, when I ran g_mindist, there was a message stating that -
"shortest periodic distance is 1.39714 (nm) at time 21824 (ps), between atoms 2062 and 3688" where 2062 is a protein atom and 21824 is a water molecule. I wanted to know why this happens in spite of taking care of it earlier. what are the consequences, what is the solution? Thanking you kavya
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