[gmx-users] restraining to center of geometry?

Michael Shirts mrshirts at stanford.edu
Sun Jan 25 04:01:01 CET 2004

Hello, all-

So, supposing I had a protein, and wanted to restrain a ligand by attaching
it with a spring to some point that wasn't actually an atom -- say it was
the center of geometry of a number of atoms around the binding pocket, so that
it's a point that redefines itself at each step of the simulation.

1) Is this possible to do using either the position restraint or distance
restraint tools in GROMACS?

2) If not, how might one modify the code to put this in?

Michael Shirts
Stanford University.

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