[gmx-users] Umbrella sampling along collective coordinate

[James Starlight]

Dear Gromacs users!


I'm intresting in running of the umbrella sampling simulation to calculate
of the PMF along eigenvector using as the reaction coordinate.
In case of my study I'd like to estimate free energy of transition R -> R*
(activation of the receptor) having eigenvector represented as the possible
path beetween both of the initial sub-states ( in that case conformation
transition from non-active to active receptor state).
>From Gromacs manual I've found that conformational flooding method could be
used for such umbrella simulation in case of harmonic potential application
on the eigenvectors. Now If I extract 5 conformations (=5 umbrella windows)
along this eigenvector and restried system in different positions along
this eigenvector. Might I apply WHAM method to analysis of the convergence
of such 5 simulations to reproduce PMF?

Thanks for suggestions,

James