Hi,
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 ?
Sanku
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