[gmx-users] Free energy perturbation of Cu(I) binding

[chris.neale at utoronto.ca]

You might benefit from reading Mobley, Chodera, and Dill. J. Chem.  
Theory. Comput. 2007, 3, 1231-1235.

This paper doesn't relate exactly to your question, though, unless you  
do something like David initially suggested here  
http://www.gromacs.org/pipermail/gmx-users/2009-February/039436.html  
to get some metastable state in the absence of copper.

Chris.


-- original message --

Hey Mark,
  I am just not getting the theory behind doing position restraints and
applying them to equilibrate. So let me frame my question well. Cu(I)
is binding to three amino acids in the protein. Now If I remove Cu(I)
the -1 charge of the protein changes to 0. So the protein has two
specific charge states which it should equilibrate. So coming to
position restraint should I restrain the total protein when I remove
Cu from the structure or just the copper binding core and how does
restraining help the protein from destabilizing due to huge
electrostatic interactions. I looked for this in the manual but could
not understand it properly and was not sure what I am doing.
Please help me out here.
Thank you
abhigna