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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.

update:

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.

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  • $\begingroup$ Is there a reason why you need to use ASE? $\endgroup$ Commented Jun 7, 2023 at 11:58
  • $\begingroup$ I can help you if you can provide an example of your pdb file (e.g. the first 2 snapshots of your trajectory). $\endgroup$
    – Shaun Han
    Commented Jun 8, 2023 at 3:50
  • $\begingroup$ @HemanthHaridas, I have experience in the post-processing of trajectories in ASE. Also, I have some specific code written for some analysis. What do you use in your case? $\endgroup$
    – Saha_1994
    Commented Jun 8, 2023 at 11:08
  • $\begingroup$ @ShaunHan, I appreciate your text. Here is the google drive link, drive.google.com/file/d/1JFXotd1GKD6m1Vzib3SjFAl67zFlK0f-/… $\endgroup$
    – Saha_1994
    Commented Jun 8, 2023 at 11:11
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    $\begingroup$ @Saha_1994 You may check the GromacsWrapper package. $\endgroup$ Commented Sep 14, 2023 at 11:08

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