Monday, October 11, 2010
Wednesday, September 15, 2010
Ascalaph: Ascalaph 1.7.7 released
Ascalaph: Ascalaph 1.7.7 released: "Ascalaph 1.7.7 with Sheffield implicit water model released http://www.biomolecular-modeling.com/Purchase.html
Thursday, July 29, 2010
Ascalaph 1.7.1
Allow me to introduce the programs of molecular modeling Ascalaph and Abalone.
It seems to me that starting with version 1.7, they reached a state when they can be useful for general application. The idea behind these programs is to have a graphical system for molecular mechanics, in particular under Windows.
The programs are very similar. But Ascalaph mainly plays the role of a graphical environment for the well-known packages of molecular mechanics and quantum chemistry, while Abalone relies on their own systems of molmechanics.
Much attention is paid to design the initial models. Molecules can be drawn by hand, then put in the minimal reasonable conformation with aid of rough optimization, and then optimized by quantum-chemical methods. There is a constructor of chain molecules, which allows to create a model with pre-installed molecular-mechanical parameters form the residues. Users can create their own residues and add them to the database. There is a procedure for adding the box with a solvent, such as a water. This box should be made separately and then added to the model. The overlapping solvent molecules can be automatically removed.
Interface with quantum chemical programs primarily designed to develop the parameters of molecular mechanical force fields. Currently supported NWChem, CP2K and PC GAMESS/Firefly.
- Optimization
- Molecular dynamics with multiple time steps, second and fourth order symplectic integrators
- Hybrid Monte Carlo
I hope you enjoy these programs and will be grateful for comments and suggestions.
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