[gmx-users] How to get centre of mass bond & angle distribution

jagannath mondal jmondal2004 at yahoo.co.in
Tue Nov 3 06:37:33 CET 2009

  I am trying to coarse-grain a system. For that I want to optimize the bond , angle and dihedral parameters of coarse-grained model based on atomistic simulation. For that, in the atomistic simulation part, I want to calculate the the distribution of 'effective' angle made by the 'centre of mass' of the atoms used for coarse-graining ( in stead of using one of the representative atoms used for coarse-graining ). For example, if I have a molecule  H3C-CH2-CH3,  I want to calculate the angle-distribution of   H3C-CH2-CH3  in stead of C-C-C and bond-distribution of H3C-CH2 in stead of C-C .
But I do not know how can I invoke the centre of mass of a group of atoms in the index file for g_angle or g_bond.
Do I need to create some dummy atoms? If so, how can I do that? 
Any help will be highly appreciated.

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