It appears that you are working with big MD trajectory files, and the visual aids are not working properly due to RAM constraints. Trajectory file splitting is a workable solution, but it necessitates managing topology and trajectory files carefully. Here's how to use GROMACS to manage big trajectory files step-by-step:

Splitting Trajectory Files:

2 Generate New Topology:

• When you split the trajectory, you need to create a new topology file for each segment. Use the original topology file (MD.tpr) for each segment;
• gmx grompp -f md.mdp -c traj_part1.gro -p topol.top -o md_part1.tpr

Repeat for Each Segment:

• Repeat the above steps for each segment of the trajectory.

Create MD Movie from Segmented Trajectories:

Now that you have segmented trajectory and topology files, you can try creating an MD movie for each segment and then concatenate them.

Create MD Movie for Each Segment:

• Use GROMACS to create MD movies for each segmented trajectory:
• gmx mdmat -f traj_part1.xtc -s md_part1.tpr -nice 0 -o mdmovie_part1.xpm

Concatenate MD Movies:

• After creating MD movies for each segment, you can use a tool like convert from ImageMagick or ffmpeg to concatenate individual movies into a single movie:
• convert mdmovie_part1.xpm mdmovie_part2.xpm ... mdmovie_final.gif

Visualization:

• Finally, you can use a lightweight visualization tool, such as VMD, PyMOL, or UCSF Chimera, to open and visualize the final concatenated MD movie.

Note:

• Ensure that the split trajectories have proper continuity (overlapping frames between segments) to avoid artifacts during concatenation.

This approach helps in dealing with large trajectory files and limited system resources. Adjust the parameters like start_frame, end_frame, and skip_frames according to your requirements and system limitations.