Changing Bead Colors for Tracking Polymer Chains in LAMMPS DPD Simulation: Seeking Tool Recommendations

Hi everyone,

I am currently working on a Dissipative Particle Dynamics (DPD) simulation using LAMMPS, and my system involves 81,000 beads representing a mixture of water and surfactant beads. My current objective is to track the behavior of a specific polymer chain within this intricate system over time. To achieve this, I need to alter the color representation of the beads corresponding to this particular polymer chain in the LAMMPS output. This color modification is crucial for distinguishing the chain from other particles, allowing me to tag and track its dynamics throughout the simulation. Could you please provide guidance on how to modify the color of individual chains in LAMMPS for this purpose?

Additionally, if there is a specific tool you recommend for visualizing and tracking the polymer chain in DPD simulations, I would greatly appreciate your suggestions.

Thank you for your time.

I think this is more a visualization question than a LAMMPS question. I am confident that in the two most popular visualization tools for LAMMPS trajectories, OVITO and VMD, you can select and highlight individual chains/molecules through their selection language and ability to build a visualization from multiple representations. I am most familiar with VMD and there it is definitely possible to set something like that up (and much more complex things). A long time ago (20+ years), I wrote a tutorial website for using VMD with CPMD to visualize complex information. And there you don’t have options like assigning a molecule ID or similar. It is still online at: Visualization and Analysis of Quantum Chemical and Molecular Dynamics Data with VMD

I am certain, similar things can be done with OVITO.

You can follow @akohlmey’s tutorial on VMD or use OVITO for that.

In OVITO, you can select your particles using their IDs or molecule attribute with the expression selection tool and generate trajectory lines with the generate trajectory lines for your selection. It is pretty straightforward.

What you need from LAMMPS though are dumps of your trajectories, that is, coordinates of your atoms to be read in VMD or OVITO. Not images to which you alter the color.