1-2, 1-3, 1-4 pairwise interactions | special_bonds |
2d simulations | fix enforce2d, Section_howto howto_2 |
AI-REBO potential | pair_style airebo |
AMBER force field | special_bonds |
angle potentials | angle_style |
aspherical particles | Section_howto howto_14 |
atom properties | atom_style |
atom to continuum coupling | fix atc |
barostatting | Section_howto howto_16 |
bcc lattice | lattice |
bead-spring model | bond_style fene |
bond breaking | fix bond/break |
bond creation | fix bond/create |
bond potentials | bond_style |
bond swapping | fix bond_swap |
bond-order potentials | pair_style tersoff, pair_style meam, pair_style reax |
box deformation | fix deform, Section_howto howto_12 |
Buckingham potential | pair_style buck |
center-of-mass | compute com |
centro-symmetry factor | compute centro/atom |
CFG file output | dump cfg |
CHARMM force field | pair_style charmm, special_bonds |
class 2 potentials | pair_style class2, bond_style class2 |
CNA = common neighbor analysis | compute cna/atom |
colloidal particles | atom_style colloid |
COMPASS potentials | pair_style class2, bond_style class2 |
conjugate gradient minimization | min_style cg |
continuum coupling | fix atc |
coordintation number | compute coord/atom |
cubic lattice | lattice |
DCD file output | dump dcd |
Debye screening | pair_style lj |
delete bonds | delete_bonds |
depositing atoms | fix deposit |
diffusion coefficient | compute msd |
dihedral potentials | dihedral_style |
dipole moments | dipole, pair_style dipole/cut, atom_style dipole |
DPD = dissipative particle dynamics | pair_style dpd |
DSMC = Direct Simulation Monte Carlo | pair_style dsmc |
dump file output | dump |
EAM = embedded atom method | pair_style eam |
electric field application | fix efield |
energy minimization | minimize |
evaporating atoms | fix evaporate |
Ewald sums | kspace_style |
excluded pair interactions | special_bonds |
fcc lattice | lattice |
FENE bead-spring model | bond_style fene |
g(r) | compute rdf |
GayBerne potential | pair_style gayberne |
geometric regions | region |
grain boundary creation | lattice, create_atoms |
grain boundary forces | fix orient/fcc |
granular particles | atom_style granular |
gravity | fix gravity |
GROMACS force field | pair_style gromacs |
groups of atoms | group |
heat flux calculation | compute heat/flux |
heirarchical time stepping | run-style respa |
hexagonal lattice | lattice |
hybrid potentials | pair_style hybrid, bond_style hybrid |
improper potentials | improper_style |
integrate | run |
interactive visualization | fix imd |
kinetic energy | compute ke, compute ke/atom |
Langevin thermostat | fix langevin |
lattices of atoms | lattice |
long-range Coulombics | kspace_style |
lubrication potential | pair_style lubricate |
MEAM = modified EAM potential | pair_style meam |
mean-squared displacement | compute msd |
Morse potential | pair_style morse |
neighbor lists | neighbor, neigh_modify |
NEB = nudged elastic band | neb |
NEMD = non-equilibrium MD | Section_howto howto_13 |
Newtons law | newton |
non-orthogonal simulation boxes | Section_howto howto_12 |
Nose/Hoover barostat | fix npt |
Nose/Hoover thermostat | fix nvt |
NPH ensemble | fix nph |
NPT ensemble | fix npt |
nudged elastic band | neb, fix neb |
NVE ensemble | fix nve |
NVT ensemble | fix nvt |
out-of-plane potentials | improper_style |
parallel tempering | temper |
Peridynamics | pair_style peri/pmb |
periodic boundary conditions | boundary |
PME = particle-mesh Ewald | kspace_style |
point dipoles | dipole, pair_style dipole/cut, atomstyle dipole |
potential energy | compute pe, compute pe/atom |
PPPM = particle-particle particle-mesh | kspace_style |
PRD = parallel replica dynamics | prd |
pressure | compute pressure, compute stress/atom |
radial distribution function | compute rdf |
radius of gyration | compute gyration |
ReaxFF potential | pair_style reax |
REBO potential | pair_style airebo |
replica exchange | temper |
replicate a system | replicate |
REsquared colloidal potential | pair_style resquared |
rigid bodies | fix rigid, fix poems |
rigid ion potential | atom_style charge, pair_style buck/coul/long, set charge |
rRESPA time stepping | run_style respa |
SHAKE constraints | fix shake |
SLLOD | fix nvt/sllod |
snapshot file output | dump |
spatial averaging | fix ave/spatial |
SPC water | Section_howto howto_9 |
spherical particles | Section_howto howto_14 |
spring force constraints | fix spring, fix spring/rg, fix spring/self |
square lattice | lattice |
steepest descent minimization | min_style sd |
steered MD | fix smd |
Stillinger-Weber potential | pair_style sw |
stochastic rotation dynamics (SRD) | fix srd |
stress/strain calculations | fix deform |
tabulated potentials | pair_style table, bond_style table, angle_style table |
TAD = temperature accelerated dynamics | tad |
targeted MD | fix tmd |
temperature | compute temp, compute temp/com, compute temp/sphere, compute temp/partial |
tempering | temper |
Tersoff potential | pair_style tersoff |
thermal conductivity calculation | fix thermal/conductivity |
thermodynamic output | thermo, thermo_style |
thermostatting | Section_howto howto_16 |
time averaging | fix ave/time |
time integration | run_style, run |
timestep | timestep, fix dt/reset |
TIP3P water | Section_howto howto_7 |
TIP4P water | Section_howto howto_8 |
torsional potentials | dihedral_style |
triangular lattice | lattice |
triclinic simulation boxes | Section_howto howto_12 |
two-temperature electron model | fix ttm |
umbrella sampling | fix spring |
velocity setting | velocity |
Verlet time integration | run_style verlet |
virial computation | compute presure, compute stress/atom |
viscosity calculation | fix viscosity, fix deform, fix nvt/sllod |
viscous drag | fix viscous |
visualization | Section_howto howto_11 |
walls | Section_howto howto_17 |
Yukawa potential | pair_style yukawa |