Hi everyone, I have a question about -nmol option of g_gyrate -h :
With the -nmol option the radius of gyration will be calculated for multiple molecules by splitting the analysis group in equally sized parts. If there are 4 chains ABCD in the solvent, and each chain has n atoms of different types numbered as : A_1 to A_n, B_n+1 to B_2n, C_2n+1 to C_3n and D_3n+1 to D-4n.. defining all these atoms in group [4 polymer chain atoms] together with -nmol option of g_gyrate gives average Rg of each chain? Is the program really able to tell 4 chains apart and what it reports is wrt center of mass of each chain? or it takes all atoms of [4 polymer chain atoms] and computes a new center of mass for the union of all chains..!? >From -nmol option I got 1.4 nm but averaging over each chain separately gives 1.9 nm which I think shows a significant difference. Can you please also clarify what do principle axis and RgX, RgY...refer to? and my last question is what -p option of g_polystat gives is wrt to which axis? principle or the average of RgX, RgY, RgZ? Many thanks for your help. Best,
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