Units and constants
The units of MDAnalysis trajectories are the Å (ångström) for length and ps (picosecond) for time. Regardless of how the original MD format stored the trajectory data, MDAnalysis converts it to MDAnalysis units when reading the data in, and converts back when writing the data out. Analysis classes generally also use these default units. Exceptions to the default units are always noted in the documentation; for example, mass densities can be given in \(g/cm^3\).
Other base units are listed in the table Base units in MDAnalysis.
Quantity |
Unit |
SI units |
|---|---|---|
length |
Å |
\(10^{-10}\) m |
time |
ps |
\(10^{-12}\) s |
energy |
kJ/mol |
\(1.66053892103219 \times 10^{-21}\) J |
charge |
\(e\) |
\(1.602176565 \times 10^{-19}\) As |
force |
kJ/(mol·Å) |
\(1.66053892103219 \times 10^{-11}\) J/m |
speed |
Å/ps |
\(100\) m/s |
mass |
u |
\(1.66053906660(50) \times 10^{-27}\) kg |
angle |
degrees |
\(\frac{\pi}{180}\) rad |
Unit conversion
Quantities can be converted from units with convert().
convert() simply multiplies the initial quantity with a
precomputed conversion factor, as obtained from
get_conversion_factor().
The computed conversion factors for each quantity type are stored in MDAnalysis.units and shown below.
Constants
Length
Unit
Conversion factor
A
1
Angstrom
1
angstrom
1
femtometer
100000
fm
100000
nanometer
0.1
nm
0.1
picometer
100
pm
100
Å
1
Density
Unit
Conversion factor
A^{-3}
1
Angstrom^{-3}
1
Molar
1660.54
SPC
30.3718
TIP3P
29.8566
TIP4P
29.8864
nanometer^{-3}
1000
nm^{-3}
1000
water
30.0063
Å^{-3}
1
Time
Unit
Conversion factor
AKMA
20.4548
femtosecond
1000
fs
1000
microsecond
1e-06
millisecond
1e-09
ms
1e-09
nanosecond
0.001
ns
0.001
picosecond
1
ps
1
s
1e-12
sec
1e-12
second
1e-12
us
1e-06
μs
1e-06
Charge
Unit
Conversion factor
Amber
18.2223
As
1.60218e-19
C
1.60218e-19
e
1
Speed
Unit
Conversion factor
A/AKMA
0.0488882
A/fs
1000
A/ms
1e-09
A/ps
1
A/us
1e-06
Angstrom/AKMA
0.0488882
Angstrom/femtosecond
1000
Angstrom/fs
1000
Angstrom/microsecond
1e-06
Angstrom/millisecond
1e-09
Angstrom/ms
1e-09
Angstrom/picosecond
1
Angstrom/ps
1
Angstrom/us
1e-06
Angstrom/μs
1e-06
angstrom/femtosecond
1000
angstrom/fs
1000
angstrom/microsecond
1e-06
angstrom/millisecond
1e-09
angstrom/ms
1e-09
angstrom/picosecond
1
angstrom/us
1e-06
angstrom/μs
1e-06
m/s
100
nanometer/picosecond
0.1
nanometer/ps
0.1
nm/ns
100
nm/ps
0.1
pm/ps
100
Å/ps
1
Force
Unit
Conversion factor
J/m
1.66054e-11
N
1.66054e-11
Newton
1.66054e-11
kJ/(mol*A)
1
kJ/(mol*Angstrom)
1
kJ/(mol*nm)
10
kJ/(mol*Å)
1
kcal/(mol*Angstrom)
0.239006
Energy
Unit
Conversion factor
J
1.66054e-21
eV
0.0103643
kJ/mol
1
kcal/mol
0.239006