[gmx-users] Umbrella sampling along collective coordinate

[James Starlight]

More specifying my question:

I calculated 10 umbrella windows using flooding aproach (applied restrained
harmonic potential on the reaction coordinate)

what are the output data from such restraining flooding could be useful for
WHAM assuming that typical EDI output  consist time-dependent dynamics of
4 below variables

RMSD to ref
EV1prjFLOOD
 EV1-Vfl
   EV1-FLforces

should I provide to WHAM  the EV1-FLforces dependence on time?

James



2013/11/19 James Starlight <jmsstarlight at gmail.com>

> 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
>