I am trying to study some trajectories generated using Gromacs. I have been given tpr and pdb files of the simulation. What might be the most effective way to load them in ASE? Or is there way to convert them to traj format?
I tried converting pdb to traj, but the system size being of the order of 1000 atoms slows the process alongside missing energies due to no calculator from pdb file? (my guess it might need more file)
Thanks for your attention.
from ase import io # Load the PDB or GROMACS trajectory file traj = io.read('./em.gro', index=':') # replace with 'trajectory.gro' for GROMACS # Write out the trajectory in the ASE trajectory format io.write('check.traj', traj)
I tried doing this way, but I see no energy due to no calculator information. Also, it is painfully slow.