Automatic bind selection in vmd for lammps trajectories

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1

Dear all,

I have my output lammps trajectories in .dump files and I would like to know how to only allow visualisation of bonds between consecutive beads of a polymer chain. It seems to me that I need to disable automatic bonds, but I am not sure how this can be achieved. Thank you for any input.

2

Dear all,

I have my output lammps trajectories in .dump files and I would like to know how to only allow visualisation of bonds between consecutive beads of a polymer chain. It seems to me that I need to disable automatic bonds, but I am not sure how this can be achieved. Thank you for any input.

that depends on the visualization tool you are using.
this has nothing to do with lammps. lammps only
spits out the positions of the atoms.

axel.

3

Thank you Dr Axel, I forgot to mention I am using vmd. I should have posted the question to the vmd list...

4

Thank you Dr Axel, I forgot to mention I am using vmd. I should have posted the question to the vmd list...

in vmd you can determine the bonding pattern by
loading a suitable topology file first. vmd will only
guess bonds, if they are not present.

axel.