I was setting up a simulation of a 16 bp ssDNA in a box of water, and when I visualized the .gro file after the NVT equilibration using VMD, it seems one of the bonds had disappeared from the visualization. So far, I’d been following the procedure in the first GROMACS tutorial up to the NPT equilibration step and have been using the same mdp parameters, does anyone know whether this is indicative of something going wrong in the simulation and how to fix it?
The gro file has only coordinates and no bond linkage info. VMD uses a distance-based heuristics which means that two atoms within a given distance will be shown as bonded. You can see all tyles of artefacts based on this e.g., hydrogen bonded to 2 atoms! Don’t worry as long as the topology file is correct.
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That’s a relief, thanks for the reply!