Typically, the mdrun command of gromacs whether in the energy minimization, equilibration or production stage generates several files containing different types of information. These include:

• Trajectory file: This file, usually with .trr extension, stores the positions, velocities, and optionally forces of the simulated system at discrete time points throughout the simulation. It's crucial for analyzing the system's dynamics and visualizing its motion.

• XTC (eXtended Trajectory Coordinates) file: An alternative trajectory file format, similar to TRR, but with reduced precision to save disk space. It contains coordinates and possibly velocities of atoms at each time step.

• Energy file: This file, often with .edr extension, records various energies and other thermodynamic properties like temperature, pressure, and potential energies during the simulation. It helps understand the system's energetic behavior and identify potential problems.

• Log file: This file, typically named mdout.log, logs the overall progress of the simulation, including initialization details, warnings, and timing information. It's useful for troubleshooting and keeping track of the simulation steps.

• Structure file: This file, commonly with .gro extension, contains the final coordinates and velocities of the system at the end of the simulation. It serves as a starting point for further simulations or analysis.

• Checkpoint file: This file has the .cpt extension. If the simulation is interrupted, a checkpoint file can be used to resume it later from the same point.

However, while energy minimization in GROMACS typically uses mdrun, it doesn't actually run a full simulation, hence omitting the .xtc file by default. To generate an .xtc file during energy minimization using mdrun, you have two options:

1. Utilize nstxout-compressed parameter:

• Edit the molecular dynamics parameters (mdp) file for energy minimization (usually named em.mdp)

• Add the nstxout-compressed to your em.mdp file directly under the nsteps parameter and set it to a desired value. A value of 1 will capture every frame, while higher values will output less frequently. Choose a value suitable for your analysis needs and computational resources. The value of 10 will make sense for a 50000 energy minimization steps. I.e. nstxout-compressed = 10

• Run mdrun with the modified em.mdp file. This will now write both the .trr and .xtc files as specified by nstxout-compressed.

2. Employ grompp and trjconv tools:

• If you don't want to modify the original simulation settings, you can use a post-processing approach.

• Run grompp with the minimization .mdp file to generate a .tpr (topology parameters) file.

• Use trjconv to convert the resulting .trr file to an .xtc file. Here's the basic command:

trjconv -f minim_md.trr -o minim_md.xtc -p minim.tpr

Note: rename the minim_md.trr file to what you have.

Alternatively, you can directly generate the RMSD data from your .trr trajectory file without needing the .xtc file. Here are several ways to achieve this:

Using GROMACS tools:

• gmx rms: This is the most common way to calculate RMSD in GROMACS. You'll need the .trr file, a reference structure file (usually .gro), and optionally an index file if you want to calculate RMSD for specific groups of atoms. Here's the basic command:

gmx rms -s ref.gro -f my_traj.trr -o rmsd.xvg

Again, remember to rename the .gro and .trr files to what you have.

• gmx trjconv: While not directly calculating RMSD, you can use trjconv to convert your .trr file to other formats like .pdb or .gro depending on your preferred analysis software. These formats are readily accepted by various tools for RMSD calculations.

Using third-party software:

• VMD/PyMOL: These popular molecular visualization tools can directly load .trr files and offer built-in functionalities to calculate RMSD for different atom selections.

• MDAnalysis: This Python library allows reading and manipulating .trr files and includes functions for RMSD calculations.

This should solve your problems.

you repeat all steps maybe problem in protein prepration step. kindly check or in prepration step add -i. As per your question the experiment not proceed because as you say no xtc file.

thank you Emmanuel Onah for your detailed answer. i used the following script for energy minimization. I will add the nstxout-compressed to see whether it produces the xtc file or not. see confly I have tried using .trr file but it contains only one frame. although my log file contains information for about 473 steps.

; minim.mdp - used as input into grompp to generate em.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Minimization step size nsteps = 50000 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ; Buffered neighbor searching ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.0 ; Short-range electrostatic cut-off rvdw = 1.0 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions