[gmx-users] Query on restraining center of mass of a protein

Sanku M msanku65 at yahoo.com
Tue Nov 15 00:21:25 CET 2011

  I have a system containing water and a large protein. In the simulation, I do not want the protein center of mass to drift away. I was wondering what will be the reasonable method in gromacs to fix the position of the center of mass of the protein in its original position . I was thinking about two options in gromacs.
  1) use the protein as comm-grp only to remove its center of mass motion . ( or should I use both protein and non-protein ( water) center of mass as comm-grps separately ).
  2) Finding the residue closest to center of mass of the protein ( but I am not sure how to do it ).
Can anyone suggest which will be a good idea ?

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