Is PBC correction needed before Peak force, total work, RMSD analysis and trajectory visualization?

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GROMACS version:
GROMACS modification: Yes/No
Hello everyone,

I recently completed a steered molecular dynamics simulation of a protein–protein complex using periodic boundary conditions.

Now I want to calculate RMSD and visualize the trajectory. I am a bit confused about which trajectory file I should use.

Can I directly use the raw smd.xtc trajectory with the smd.gro/smd.tpr file, or should I first apply PBC correction using gmx trjconv?

Specifically,

  1. Is PBC correction mandatory before RMSD calculation?

  2. Is PBC correction necessary before visualizing maximum force/peak force, for the force time profile, and total mechanical work?

  3. If the complex does not visibly jump across the box boundary, is it still necessary?

  4. For SMD, should I center and fit the trajectory on the restrained/pulled reference group, such as MHC or receptor, before calculating RMSD?

I am new to MD trajectory analysis, so I would appreciate any guidance on the correct workflow.

2

Hi @rachana

So

  1. Usually yes, as the RMSD tools not always take into account PBCs. Typically this gives rise to sharp jumps in the RMSD values from a frame to the next one.

  2. The force is usually collected in some xxx-pullf.xvg file. These values do not need (and can’t) be corrected, these are calculated on the fly during the run.

  3. Probably no, but you do not need to jump across a boundary, it is sufficient to have part of the entity of which you are calculating the RMSD crossing to compute wrongly RMSD.

  4. Same as above. Fitting and centering is not mandatory, but correcting for PBCs is usually necessary.

In general some level of post-processing of the trajectory is always suggested, especially for visualization purposes. PBC corrections are usually the first step, perhaps performed together with the centering. Finally, the fit is very helpful for systems in water, as they will tumble around all the time. Most of the post-processing depends on your targets and what you want to analyze and plot.

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