HI What is the math definition of the radii of gyration about the principal axes in Gromacs?
I use the command g_gyrate -p For lysozyme , I got => 0.922754 1.22249 1.25603 but in some paper, the authors got => 0.660 0.833 0.991 It is a quite difference. >From David => "The difference seems to be a constant factor. Gromacs computes sqrt (sum m (r-r_com)^2 / sum m) I'm pretty sure it says so in the manual." 1. so the different factor is sum m , not sum_N, right ? (N= number of atoms) 2. the choice of the principal axes of the protein molecule is a standard process ? => I mean the principal axes of the protein molecule is fixed, right ? => I mean the math of the principal axes of the protein molecule is defined all over the world , right ? Thank you Lin On 2010-08-14 23.49, Chih-Ying Lin wrote: > > > > Hi > To Calculate the radii of gyration about the principal axes > > I use the command > g_gyrate -p > > For lysozyme , I got => > 0.922754 1.22249 1.25603 > > but in some paper, the authors got > => 0.660 0.833 0.991 > > It is a quite difference. > > what is the definition of the radii of gyration about the principal axes ? > i have checked the Gromacs manual but see nothing there. The difference seems to be a constant factor. Gromacs computes sqrt (sum m (r-r_com)^2 / sum m) I'm pretty sure it says so in the manual. > > > Thank you > > Lin >
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