I ran an example input file “in.tiny_polystyrene.stabilized’ located in a directory examples/PACKAGES/reaction/tiny_polystyrene shipped with Lammps version 8Feb2023
The log file shows that the system has reacted with reaction values for f_rxn, f_rxn and f_rxn. When visualizing the trajectory, I was hoping to see some polyester chains. Instead I see only the monomers in a box.
I visualised the system in vmd by loading the dump file that had following attributes
id, type, mol, x, y , z, ix, iy, iz dumped at every 100 fs. The system was run for a total of 50000 fs.
Coordinates were dumped for group “all” . I also dumped the coordinates separately for “bond_react_MASTER_group” and visualised in vmd with no luck.
The bonding information is not included in your dump file, so how should any software know about changing bonds?
Besides VMD assumes that the bonds don’t change. It will create an initial bond topology for visualization purposes based on atom distance heuristics. VMD has a Dynamic Bonds representation that can do the same dynamically when animating a trajectory.
You may consider using OVITO instead, which has different defaults (but is slower in switching between animation frames).
Thanks for the reply.
Even if the bonds are not explicitly listed in dump file, shouldn’t the monomers that are part of the polymer chain appear closer? Which doesn’t seem to be the case. Monomers are very far apart, even though the output from dump file shows that they share the same molecule id, and therefore belong to the same polymer.
Visualization is very insensitive to small changes. You have to keep in mind that the example simulations are mostly meant to show the typical syntax and structure of an input file, not as a full example of a production style simulation. The simulation in the example you are looking at, is only run for 10000 MD steps which corresponds to 10ps. Not much can happen in 10ps.
But if you comment out the last line that writes out a data file of the final state, you can see that the number of bonds has changed from the initial data file from 320 to 334, the number of angles from 480 to 564, the number of dihedrals from 640 to 862 and the number of impropers from 160 to 132. So there are definitely reactions happening. If you look at the thermo output you see that confirmed.
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