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Disclaimer: I am new to VMD and molecular dynamics.

I am currently working on a simulation of a very basic coarse-grained model of DNA (or rather ssDNA because every base pair is a single bead). This far I have visualized the trajectories of my simulations producing a trr file and a pdb file in which I represent every bead with some atom and I specify all the links. This is ok in the sense that it allows me to visualize it but I was wondering what better ways are there to do this. Is there some way of creating custom beads of arbitrary size and color for example so that I can distinguish among the different nucleobases?

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    $\begingroup$ VMD's Graphical Representations allow you to do so. You make the necessary selections on the VMD, and then you can color or represent it accordingly. $\endgroup$
    – Roshan Shrestha
    Feb 3 at 13:47
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    $\begingroup$ Here you can find at least two tutorials that used VMD to analyze coarse-grained models. $\endgroup$
    – Camps ♦
    Feb 3 at 14:12
  • $\begingroup$ Also it's worth making sure you're not reinventing the wheel -- there is an excellent set of CG DNA models under the oxDNA family; the LAMMPS implementation should be quite fast and there are automatic visualisation settings for Chimera. $\endgroup$
    – Shern Ren Tee
    Feb 4 at 6:55

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