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
$[\mathrm{area}]$	$\mathrm{Å}^2$	$\mathrm{nm}^2$
$[\mathrm{volume}]$	$\mathrm{Å}^3$	$\mathrm{nm}^3$
$[\mathrm{time}]$	48.8882129 fs	1 ps
$[\mathrm{velocity}]$	0.02045482828 Å/fs	1 nm/ps
$[\mathrm{force}]$	kcal/mol/Å	kJ/mol/nm
$[\mathrm{pressure}]$	68568.4230 atm	16.3882464 atm
$[\mathrm{charge}]$	0.05487686461 e	0.0848385920 e
$k$ (Boltzmann’s constant)	0.00198720426 kcal/mol/K	0.00831446262 kJ/mol/K