Reference manuals - Nemesis -1Petr
Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kotlářská 2, CZ-61137 Brno
Nemesis
Reference manuals
Reference manuals - Nemesis -2-
Nemesis
Reference manuals - Nemesis -3-
Nemesis
Starting the program:
$ module add nemesis
$ nemesis
Mouse:
Left mouse button selection
Middle mouse button rotation
Right mouse button translation
Scroll wheel zoom
Modifiers:
Shift XZ -> Y moves
Ctrl toggles between secondary and primary manipulator
Reference manuals - Nemesis -4Nemesis
- Build Project
layers
graphic models
molecule construction/editing
geometry measurement
Force field settings for optimization: menu Geometry-> Optimizer Setup
geometry optimization
using a force field
Reference manuals - Nemesis -5Geometry
optimization visualization
1) Project: Trajectory
2) Fille-> Import Trajectory as -> Gaussian Geometry Optimization
double click
double click
optimization process
Reference manuals - Nemesis -6Vibration
visualization
1) Project: Trajectory
2) Fille-> Import Trajectory as -> Gaussian Vibrations
double click double click
choose a vibration
start the animation