From: Branko (
Date: Fri Nov 19 2010 - 12:44:50 CST


I use gyration as colvar (in combination with distance) to obtain 3D
free energy surface for set of molecules. Gyration -- colvar as defined
in NAMD manual do not include masses of atoms included.

When I analyze trajectory and measure rgyr of atoms defined by colvar
used, accordance is OK, as far as heavy atoms Br and Cl are not part of
molecule. Please let me know next:

1. Is colvar used in ABF include atomic masses (if atoms are described
as "atomNumbers"), or simply measure radius of gyration of atomic
positions (providing that every position have a same weight).

   2. How (explicitly) to include mass as weighting factor in script
      that you made previously.
   3. Is "measure rgyr selection" (providing that selection is "index")
      give output comparable with colvar that I use in ABF calculation
      (see under 1).