NVT molecular dynamics by the Nose-Hoover method

The Nose-Hoover molecular dynamics [20] 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 'System.Name.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. 12 (b). We see that the temperature in the molecule oscillates around the given temperature. Also for visualization of molecular dynamics, an output file 'System.Name.md' can be easily animated using free software such xmakemol [104] and XCrySDen [66] as well as NVT_VS.