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VMD cheatsheet

Create PBC

pbc box

pbc set {50 50 50}

pbc box -centersel center

PBC wrap command in vmd to re-center a protein in a simulation box

https://www.youtube.com/watch?v=IeBpVabqzy0

  • to wrap a trajectory: pbc wrap -centersel "protein" -center com -compound residue -all

  • to write dcd: animate write dcd mohamed.dcd

Visulaize LAMMPS data

topo readlammpsdata "path/to/file.lmp" topo readlammpsdata "path/to/file.data"

Write LAMMPS Data File with VMD Software

topo retypebonds

topo gussangles

topo guessdihedrals

pbc box

pbc set {50 50 50}

molinfo top set a 30.0

molinfo top set b 30.0

molinfo top set c 30.0

molinfo top set alpha 90.0

molinfo top set beta 90.0

molinfo top set gamma 90.0

topo writelammpsdata data.lammps full

Make movies

ffmpeg -i file.mpg out.mp4