SageMD is the software package for the molecular dynamic
simulation and a powerful, user friendly molecular visualization tool. Graphical
User Interface (GUI) simplifies user interaction with the MD code and provides
for setup of initial data via intuitive and easy to operate dialogues and menus.
Initial data, results, parameters, MD cell, and crystal lattice can be inspected
on the computer screen. User-friendly GUI also allows for analysis of results
with a variety of graphs and tools. SAGE MD code can be used to model properties
of materials at constant temperature and/or constant pressure, to study behavior
of the crystal lattice under expansion or compression, to calculate Radial
Distribution Function (RDF), and to derive atomic diffusion coefficients. The
user can choose different boundary conditions, namely: periodical boundary
conditions, free surfaces, and movable walls. In addition, the QEq approach for
interatomic energy calculation, which takes into account atomic charge
distribution, has been incorporated into SAGE MD code for modeling the
properties of materials with covalent chemical bonds. For derivation of atomic
charges and other parameters of force fields used in SAGE MD, quantum chemical
programs (e.g. GAUSSIAN, ABINIT) have been used.
FEATURES
- Display of 3-D graphical models of atomic structures
- Easy usage of lattice builder
- Copy, move and delete operations for selected atoms
- Option for atoms selection by means of box, sphere, cylinder and atom
type
- Selection and deselection of atoms by mouse click
- Rotating and shifting model by mouse move
- Customization of atoms color, size and the background color
- Calculation and showing bonds between atoms
- Orthogonal or perspective views of models
- Option for changing of rendering quality
- Calculation of distance and angles between atoms
- Changing atoms type of selected atoms
- Models zooming
- Exporting models to car, xtl, fdf and xyz formats
- Convenience to use the dialog to list and edit atoms position and types
- Displaying and labeling of lattice axes
- Coping of any part of the SageMD screen to the clipboard as the bitmap image
Displaying the temperature versus time graph and the structure changes
during the MD simulation
- Displaying the RDF, MSD, temperature, energy and stresses graphs after the
MD simulation
- Copying of these graphs to MS Excel and MS Word.
To learn more about SageMD see FAQs page
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