The residue numbering in a PDB file mainly depend on the person who deposited it. There are usually reasons for how things are numbered, but ultimately you should look at PDB file, and check the details on how the structure was obtained. To give you an example, during my PhD I worked on a protein that had some missing residues at the N-terminus. That was ...


No need to use gmx dump, you can simply load a xtc or trr trajectory in VMD using: vmd path/to/gro_file.gro other/path/to/trajectory_file.xtc As always you can also use the GUI to first open your gro file, then right click on the molecule and select Load data into molecule before selecting your xtc or trr file. After putting the representations as you see ...


Answer from @user1271772, converted from comment: Try on this site: https://mattermodeling.stackexchange.com/questions/tagged/gromacs. There's an entire GROMACS tag there. Answer from @vishal-kumar-sahu, converted from comment: Try running/resuming using -cpi the simulation again, I got NaN error and rerun kept continued.

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