[gmx-users] How to perform Essential dynamics sampling and cosine convergence using Gromacs 5.1

[Rakesh Ramachandran]

Dear all,

    I want to perform essential dynamics sampling using Gromacs. I have two
structures one in closed and another in open state bound with a Mg ion. I
also see the collective motion of the both the forms are in a certain
direction based on PCA analysis of md trajectories (closed to open
direction and viceversa). Now I want to perform essential dynamics sampling
for the transition from closed to open form, so what are the steps or
gromacs tools and parameters involved ?

Moreover what is the ideal way to calculate cosine convergence to know if
the simulation has converged. I read previous gromacs posts but it is very
confusing,

Regards
Rakesh