’m unable to view .xtc trajectory files from a 100 ns GROMACS simulation in PyMOL — it either crashes or gets stuck while loading. I’m not comfortable using VMD yet, and when I try to load protein-ligand complexes, only the protein is visible. Could you suggest an easier or lightweight tool for visualizing molecular dynamics trajectories, especially for protein-ligand simulations?
I feel your system configurations are not enough to handle the .xtc file.
whereas VMD can handle better than PyMol.
Regards.
@ renuka
PyMOL isn’t really built for handling big GROMACS trajectories like a 12 GB .xtc
Extract key frames 0 ns, 50 ns, 100 ns),the safest approach is to extract snapshots first then load in pymol
Please check the complextopology file first in box you create.
If in this file you see liggand and protein then proceed search
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