[gmx-users] Umbrella sampling along Radius of gyration

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Mar 29 16:50:47 CEST 2012

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).


-- original message --

   Is there any way in gromacs to use radius of gyration of a polymer  
as reaction coordinate for umbrella sampling ?

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