GROMACS File Guide

Input files

.gro - Coordinates

A fixed-column text format holding every atom's position (and optionally velocity), plus the box vectors, at a single point in time. This is what a structure "looks like" at one instant.

.top - Topology

Defines which molecules are present, how many of each, and which force field parameters (bonds, angles, charges) apply to them. If your .gro and .top disagree about how many atoms exist, grompp will refuse to run.

.mdp - Simulation parameters

A plain-text control file: integration time step, thermostat/barostat settings, number of steps to run, and how often to write output. You edit this file directly to configure a run.

.ndx - Index groups

Optional named atom subsets, letting you apply a setting - like a position restraint - to just "Protein" or just "Backbone" instead of the whole system. Not always required; GROMACS has sensible default groups built in.

The pipeline

# 1. Pre-process: combine structure + topology + parameters
gmx grompp -f minim.mdp -c system.gro -p topol.top -o em.tpr

# 2. Run: actually execute the simulation
gmx mdrun -deffnm em

.tpr - Portable run input

Produced by grompp, consumed by mdrun. A self-contained binary snapshot of everything needed to run - you can hand someone a single .tpr file and they can reproduce your run without needing your original .gro/.top/.mdp separately.

Output files

File	Contents
.log	The full run log - the first place to look when something goes wrong
.edr	Energy data (temperature, pressure, potential energy, etc.) over time
.xtc	Compressed trajectory - atom positions over time, used for analysis
.trr	Full-precision trajectory (positions, velocities, forces) - much larger than .xtc
.cpt	Checkpoint file, written periodically, lets you safely resume an interrupted run

Resuming an interrupted run

gmx mdrun -deffnm production -cpi production.cpt

Common naming convention

Most GROMACS tutorials use -deffnm to give every file from one step the same prefix (e.g. em.log, em.edr, em.tpr all belong to the "em" = energy minimization step). Keeping each stage's files under its own prefix makes a project folder much easier to navigate later.