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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
GROMACS
DL_POLY
NAMD - NAnoscale Molecular Dynamics
TINKER
MDynaMix
Others
Moltemplate
VMD TopoTools
Packmol
Avogadro
fftool
Atomsk
Aten
AtomMan
ASE - Atomic Simulation Environment
Babel
CIF2CELL
nanoSCULPT
TRAVIS - Trajectory Analyzer and Visualizer
PyLAT
MDTraj
MDAnalysis
Multiwfn
PTRAJ and CPPTRAJ
VMD - Visual Molecular Dynamics
Pymol
Ovito - Open Visualization Tool
UCSF Chimera
AIMAll
OpenBabel
Pymatgen
Ansys HFSS (FEM)
COMSOL Multiphysics (FEM)
CST Studio Suite (FDTD)
XFdtd (FDTD)
ADS - Advanced Design System (MoM)
AWR Microwave Office (MoM)
Altair Feko (MoM)
Sonnet (MoM)
Zeland IE3D (MoM)
Gaussian
VASP - Vienna Ab initio Simulation Package
ORCA
EndNote
Mendeley
Zotero
NoteExpress
ReadCube Papers