Dihedral energy extraction of atom clusters

User discussions
1

GROMACS version: 2019.3
GROMACS modification: No

Hi, is there a way to extract the dihedral energies of specified groups over time? So, for example, let’s say I have 8 united atoms in a row, and I want to group each adjacent pair of atoms into a group, so I now have 4 adjacent groups (each having 2 atoms). I then want to calculate the dihedral potential energy over the trajectory.

I’ve managed to extract the torsion angles of such groups over the trajectory, giving me some pretty good histograms. I did this by extracting the coordinates of each united atom in each frame using MDTraj in Python, then calculating the centre of mass of each group in each frame, and then used the com coordinates to calculate the torsion angle.

However I now really need to find the dihedral potential energy of such groups over the trajectory. Any help would be much appreciated.

Best regards,

Robert

2

There is no potential energy term associated with a pseudodihedral. You could do a Boltzmann weighting of the histogram to get a relative free energy profile, but there is no potential energy to extract here because there are no associated force field terms.