GROMACS version: 2023
GROMACS modification: No
Hello everyone, I hope you can help me solve a problem Gromacs generates when performing a molecular dynamics analysis: inconsistent shifts are observed in the periodic boundaries of a type of molecule composed of 19,716 atoms. The maximum distance involved in these interactions is 4312 nm, which exceeds half the length of the box. This indicates excessively large distances between atoms in bonding interactions, or that the system is exploding.
I am performing a molecular dynamics analysis for the human protein Shank 1 and the mutation of several peptides (each with a length of 5 amino acids). The dynamics generation completes without errors.
At what point does the error occur?
When generating my RMSD diagram, it stops and displays the error shown in the image.
To generate the above, I use the following code: gmx rms -s MD.tpr -f MD_NJMP_FIT.xtc -n index.ndx -o rmsd_prot_lig.xvg -tu ns
It’s important to mention three key points:
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I checked the final dynamics files with the “Chimera” viewer; the system is working correctly and doesn’t appear to be failing.
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Out of every 10 dynamics simulations I run, 2 exhibit this error.
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The dynamics process doesn’t present errors at any stage; it completes correctly.
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Recentering and adjustment are performed correctly.
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I also tried generating a larger box, but that didn’t work either. I did it with the following code:
gmx editconf -f conf.gro -c -d 1.0 -bt triclinic -o box.gro, where I already changed the value from 1 to 1.4. I don’t think the box size is the problem, as I previously performed a peptide analysis with twice the size and this error didn’t occur.
I would appreciate your opinions, advice, and strategies for resolving this error. Thank you.