GROMACS version:
GROMACS modification: No
I’m a beginner and I have PDB, GRO, and XTC files I found: Model and Data Clearinghouse. I was wondering if there was a quick way to start or rerun a simulation using these formats as inputs, rather than following all the steps in the tutorials. So far I’ve been taking the pdb file, converting it into a new gro, solvating, adding ions, running the energy minimization etc. following this tutorial: Introduction to Molecular Dynamics — GROMACS tutorials https://tutorials.gromacs.org documentation because most gromacs commands needed a topology file to run. But I assume these file formats are provided because they can be used to start some commands with?
If the coordinate file only contains the molecule without the surrounding solvent and ions, you would still need to go through the process of solvation, adding ions, etc, if your goal is to recreate the simulations or continue the simulations under some new conditions, and you’d still need to generate your own topology file if you want to run the simulations and the .top file isn’t provided.
Regarding the use of providing these file formats, given only the gro/pdb and the xtc, you can still run data analysis using the analysis modules if you want to find some information relevant to your own study but isn’t investigated in the paper, and can also use gmx trjconv to extract coordinate files of specific molecules from specific times in the trajectory to generate your own simulations. An author might also provide the data as further evidence supporting the conclusions in a paper, or someone might find a more specific use for it like using the data to train some machine learning model, etc.