It is not clear to me how one would do this with MD. The only thing
that I can think of doing in gromacs is to create a virtual particle
that is placed at the center of the protein and then apply forces
along the vector from this virtual atom to each of the Ca atoms. You
would need to modify the gromacs source code so that the Rg was
calculated at each step and the magnitude of each force is scaled
appropriately such that you get a harmonic potential about the desired
value of Rg. It should be easier to do with MC (although that's a ways
off for gromacs unless I've missed something).
Some people appear to have done exactly what you want with MD. I
presume that they used charmm.
http://www.pnas.org/content/94/19/10161.long (and their reference 22).
Chris.
-- original message --
Hi,
Is there any way in gromacs to use radius of gyration of a polymer
as reaction coordinate for umbrella sampling ?
Thanks
Sanku
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