The Nose-Hoover molecular dynamics [18] is supported to perform NVT ensemble molecular dynamics simulations by the following keyword:
MD.Type NVT_NH # NOMD|Opt|NVE|NVT_VS|NVT_NH
Then, in this NVT molecular dynamics
the temperature for nuclear motion can be controlled by
<MD.TempControl
4
1 1000.0
100 1000.0
400 700.0
700 600.0
MD.TempControl>
The beginning of the description must be '
MD.TempControl', and
the last of the description must be 'MD.TempControl
'.
The first number '4' gives the number of the following lines
to control the temperature. In this case you can see that
there are four lines. Following the number '4',
in the consecutive lines the first and second columns
give MD steps and a given temperature for nuclear motion.
The temperature between the MD steps is given
by linear interpolation.
Although the same keyword 'MD.TempControl' as used in the
velocity scaling MD is utilized in this specification, it is noted
that the format is different from each other.
In addition to the specification of 'MD.TempControl',
you must specify a mass of heat bath by the following keyword:
NH.Mass.HeatBath 30.0 # default = 20.0
In this specification, we use the unified atomic mass unit that the principal
isotope of carbon atom is 12.0.
Calculated quantities at every MD step are stored in an output
file '*.ene' as explained in 'NVT molecular dynamics by a velocity
scaling'.
As an example, we show a result for Nose-Hoover MD
of a glycine molecule in Fig. 10 (b).
We see that the temperature in the molecule oscillates
around the given temperature.
Also for visualization of molecular dynamics,
an output file '*.md' can be easily animated using free software
such xmakemol [91] and XCrySDen [61] as well as NVT_VS.