Units¶
HOOMD-blue does not adopt a particular system of units, nor does it offer a variety of systems to choose from. Instead, it follows a self-consistent system of units where all derived units (e.g. force) are defined in terms of base units (e.g. energy / length). To adopt a system of units for your simulations, choose a set of base units (e.g. meters versus centimeters for length), and then determine what the derived units are.
Base Units¶
The base units are:
\([\mathrm{energy}]\)
\([\mathrm{length}]\)
\([\mathrm{mass}]\)
Unit Conversion¶
Example unit conversions between derived units and base units:
Derived units |
Relation to base units |
|---|---|
\([\mathrm{area}]\) |
\([\mathrm{length}]^2\) |
\([\mathrm{volume}]\) |
\([\mathrm{length}]^3\) |
\([\mathrm{time}]\) |
\([\mathrm{energy}]^{-1/2} \cdot [\mathrm{length}] \cdot [\mathrm{mass}]^{1/2}\) |
\([\mathrm{velocity}]\) |
\([\mathrm{energy}]^{1/2} \cdot [\mathrm{mass}]^{-1/2}\) |
\([\mathrm{force}]\) |
\([\mathrm{energy}] \cdot [\mathrm{length}]^{-1}\) |
\([\mathrm{pressure}]\) |
\([\mathrm{energy}] \cdot [\mathrm{length}]^{-3}\) |
\([\mathrm{charge}]\) |
\(\left(4 \pi \epsilon_{0} \cdot [\mathrm{energy}] \cdot [\mathrm{length}] \right)^{1/2}\) - where \(\epsilon_{0}\) is permittivity of free space |
Common unit systems¶
Example base and derived units for common MD unit systems.
Note
All conversion factors given here are computed with Wolfram Alpha using the provided links.
Unit |
AKMA |
MD |
|---|---|---|
\([\mathrm{energy}]\) |
kcal/mol |
kJ/mol |
\([\mathrm{length}]\) |
Å |
nm |
\([\mathrm{mass}]\) |
atomic mass unit |
atomic mass unit |
\([\mathrm{area}]\) |
\(\mathrm{Å}^2\) |
\(\mathrm{nm}^2\) |
\([\mathrm{volume}]\) |
\(\mathrm{Å}^3\) |
\(\mathrm{nm}^3\) |
\([\mathrm{time}]\) |
||
\([\mathrm{velocity}]\) |
1 nm/ps |
|
\([\mathrm{force}]\) |
kcal/mol/Å |
kJ/mol/nm |
\([\mathrm{pressure}]\) |
||
\([\mathrm{charge}]\) |
||
\(k\) (Boltzmann’s constant) |