[gmx-users] Open-closed transition in a dimeric enzyme, WTM simulations

[tarak karmakar]

Dear All,
I am studying an enzyme where the closing of a loop should happen upon
ligand binding to the active site. In unbiased simulations, even after 300
ns of simulation time the loop does not close the reaction center. Thus, we
realized that the open-closed conformational change may have a high free
energy barrier, inaccessible by the unbiased trajectory. Thus, we performed
well-tempered metadynamics (WTM) simulations to study that event.

In WTM simulations, we see the opening and closing of the loop almost five
to six times within 300 ns time span. The free energy associated with this
event has barriers of only few kJ/mol (almost flat surface). Now, given
these low values of the free energy barriers, I would expect to observe the
open-closed transitions in the unbiased simulations. However, we do not see
that transition in the unbiased trajectories.

So, my questions are,
1) Are the collective variables used here inappropriate? (Although I see
the open-closed
transition a many times in the metadynamics trajectory.)

2) Is the free energy not converged? (plotting hills heights a function of
time, decays close to zero after 200-250 ns)

3) How would I make sure that the free energy is converged? (block averages
using -stride in plumed) How would I decide the blocks from the COLVAR plot?

Any suggestions would be highly appreciated.

-- 
Regards,
Tarak