[gmx-users] Trajectory guided by density maps

[Ramon Guixà]

Hi there,

I would like to use GROMACS to create a trajectory that goes from one
crystal structure to another crystal structure, both obtained from the same
system using time resolved crystallography.

Would it be feasible to use the newly implemented density-guided
simulations parameters to guide this simulation by first fitting the
initial crystal structure its density map and then switching off these
restraints while switching on the density map restraints of the second
crystal structure? I figured this would in principle create a trajectory
that better reflect the transition from one state to the other, but I am
not even sure if this makes sense at all...

Thanks in advance for the guidance,
Ramon