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

Rakesh Ramachandran korenpol3 at gmail.com
Wed Mar 30 15:59:43 CEST 2016

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


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