GROMACS version:2020.1
GROMACS modification: No
Dear Gromacs users,
I am performing a Dihedral Principal Component Analysis with Gromacs, but at the end when I get the Free Energy Landscape. How could I select the bins more representative from the trajectory from shamlog-1,2.log file? Lets say based on the energies for example or the populations?
In another words: is there a systematic method to select the bins?
A section of the
shamlog file would look like this:
Minima sorted after energy
Minimum 0 at index 301 energy 0.000
Minimum 1 at index 175 energy 0.161
Minimum 2 at index 393 energy 0.360
Minimum 3 at index 294 energy 0.520
Minimum 4 at index 400 energy 0.642
Minimum 5 at index 281 energy 0.671
Minimum 6 at index 105 energy 0.802
Minimum 7 at index 274 energy 0.812
Minimum 8 at index 219 energy 0.950
Minimum 9 at index 338 energy 1.016
Minimum 10 at index 204 energy 1.062
Minimum 11 at index 182 energy 1.155