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Contents
6.3.3 Bond polynomial force ............................................................................. 23
6.3.4 Angle harmonic force ................................................................................ 24
6.3.5 Angle cosine harmonic force .................................................................... 24
6.3.6 Angle cosine force..................................................................................... 25
6.3.7 Dihedral harmonic force ........................................................................... 26
6.3.8 Dihedral Opls Cosine force ....................................................................... 26
6.4 Integration method .............................................................................................. 27
6.4.1 Nve ensemble ............................................................................................ 27
6.4.2 Nvt ensemble with Nose Hoover method ................................................. 27
6.4.3 Nvt ensemble with Berendsen method ..................................................... 28
6.4.4 Nvt ensemble with Andersen method ....................................................... 28
6.4.5 Npt ensemble with Andersen barostat....................................................... 29
6.4.6 Nve rigid body thermostat ........................................................................ 30
6.4.7 Nvt rigid body thermostat ......................................................................... 30
6.4.8 Brownian dynamic nvt rigid body thermostat .......................................... 31
6.4.9 Nve rigid body thermostat with tunable freedoms .................................... 31
6.5 Particle Group ..................................................................................................... 32
6.5.1 Build group by keywords .......................................................................... 32
6.5.2 Build group by index range of particles .................................................... 33
6.5.3 Combine groups ........................................................................................ 33
6.6 Particle List ......................................................................................................... 33
6.6.1 Build neighbor list..................................................................................... 33
6.6.2 Build cell list ............................................................................................. 34
6.7 Data dump ........................................................................................................... 35
6.7.1 The dump of some important informations .............................................. 35
6.7.2 Configuration dump with mol2 format ..................................................... 35
6.7.3 Configuration dump with xml format ....................................................... 36
6.7.4 Configuration dump with dcd format ....................................................... 38
6.7.5 Configuration dump with binary format ................................................... 38
6.8 Some other functions .......................................................................................... 39
6.8.1 Removing the momentum of center of mass ............................................ 39