[gmx-users] REMD with umbrella sampling in Gromacs 4.5.5

[Lin, Dejun]

Hi all, 

I've read some earlier posts in the forum about replica exchange combined with umbrella sampling but still not sure if the restrain potential defined in the pull code will be included in the exchange criterion: 

P(i<->j) = min (1, exp[ (beta_i-beta_j)*(U(Ri, Dj) + U(Rj,Di) - U(Ri,Di) - U(Rj,Dj)) ] where i, j are 2 replica and beta, R, D are the respective inverse temperature, Cartesian coordinates and parameters in the pull code (force constant, equilibrium position etc.). 

Can anyone clarify that? 

Thanks, 
Dejun