LAMMPS
DL_POLY
TINKER
Others
GROMACS
NAMD
MDynaMix
Gaussian
VASP
ORCA
Moltemplate
VMD TopoTools
Packmol
Avogadro
fftool
Atomsk
Aten
AtomMan
ASE (Atomic Simulation Environment)
Babel
CIF2CELL
nanoSCULPT
TRAVIS
PyLAT
MDTraj
MDAnalysis
Multiwfn
PTRAJ and CPPTRAJ
VMD
Pymol
Ovito
UCSF Chimera
AIMAll
OpenBabel
Pymatgen
EndNote
Mendeley
Zotero
NoteExpress
ReadCube Papers