Categories
- Conferences (3)
- education (10)
- Fun (58)
- Meta (12)
- Open Access (10)
- Open Data (13)
- open science (34)
- Policy (48)
- Science (135)
- Software (633)
- Acoustics (3)
- Engineering (1)
- Physical (1)
- Speech Communication (2)
- Structural (1)
- Anthropology and Archaeology (3)
- Artificial Life (9)
- Astronomy (21)
- Aviation and Aeronautics (2)
- Chemistry (131)
- Analytical (4)
- Atmospheric (1)
- Biochemistry (6)
- Biophysical (3)
- Chemical Information (3)
- Crystallography (2)
- Electrochemistry (1)
- Molecule Viewers and Editors (39)
- Organic (2)
- Synthesis (1)
- Periodic Tables (3)
- Physical (1)
- Kinetics (1)
- Polymers (1)
- Spectroscopy (9)
- NMR (5)
- Surfaces (1)
- Theoretical and Computational (45)
- Cognitive Science (3)
- Neural Networks (2)
- Complex Systems (2)
- Computer Science (22)
- Algorithms And Computational Theory (2)
- Artificial Intelligence (4)
- Data Communication (4)
- Information Retrieval (1)
- Knowledge Discovery and Data Mining (3)
- Languages (1)
- Fortran (1)
- Measurement and Evaluation (1)
- Simulation and Modeling (2)
- Software Engineering (2)
- Symbolic and Algebraic Manipulation (1)
- Earth Sciences (19)
- Geology and Geophysics (5)
- Hydrology (5)
- Meteorology (1)
- Oceanography (3)
- Energy (3)
- Engineering (24)
- Forensics (2)
- Geography (12)
- Information Technology (1)
- Life Sciences (60)
- Bioinformatics (34)
- Ecology (5)
- Evolution and Population Genetics (3)
- Statistical (1)
- Theoretical (1)
- Genetics (9)
- Population (1)
- Medical Sciences (7)
- Physiology (2)
- Linguistics (2)
- Mathematics (108)
- Abstract Algebra (9)
- Combinatorics (1)
- Differential Equations (17)
- Fluid Dynamics (7)
- Ordinary (3)
- Partial (7)
- Dynamical Systems (4)
- Education (1)
- Geometry (3)
- Linear Algebra (26)
- Number Theory (6)
- Numerical Methods (5)
- Optimization (12)
- Probability (1)
- Set Theory (1)
- Statistics (8)
- Topology (1)
- Measurements and Units (3)
- Nanotechnology (2)
- Physics (30)
- Astrophysics (1)
- Atomic and Molecular (1)
- Computational (2)
- Condensed Matter (4)
- Dynamics (2)
- Fluid (1)
- High Energy (4)
- Magnetism (1)
- Materials (1)
- Nuclear (4)
- Optics (5)
- Plasma (1)
- Required Reading and Other Sites (25)
- Space (3)
- Tools (56)
- Numerical Libraries (8)
- Random Number Generators (2)
- Visualization (18)
- 2D Plotting (8)
- 3D Plotting (2)
- Acoustics (3)
- Uncategorized (4)
OpenScience / Software / Chemistry / Theoretical and Computational
MOPAC7
MOPAC is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. Find MOPAC7 at: http://www.ccl.net/cca/software/LINUX/mopac7/index.shtml
Posted in Ab Initio Quantum Chemistry
Leave a comment
Ghemical
Ghemical is a computational chemistry software package released under the GNU GPL. Ghemical can do all-atoms molecular mechanics (there is an experimental Tripos 5.2-like force field for organic molecules), and reduced protein models. Find Ghemical at: http://www.bioinformatics.org/ghemical/ghemical/index.html
GAMESS
The General Atomic and Molecular Electronic Structure System is a freely availible general ab initio quantum chemistry package. Free graphics programs are also availible for downloading. Find GAMESS at: http://www.msg.ameslab.gov/GAMESS/GAMESS.html
Posted in Ab Initio Quantum Chemistry
Leave a comment
AMMP Home Page
AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. Find AMMP Home Page at: http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html
Posted in Molecular Dynamics
Leave a comment
MPQC
MPQC is the Massively Parallel Quantum Chemistry Program. It computes properties of atoms and molecules from first principles using the time independent Schrodinger equation. It runs on a wide range of architectures ranging from single many-core computers to massively parallel … Continue reading
Posted in Ab Initio Quantum Chemistry
Leave a comment
Moldy
MOLDY is a parallelised OpenMP short-ranged molecular dynamics program, first written at Harwell Laboratory in the 1980s. The program is rewritten in a modular fashion to allow for easy user modification, in particular the implementation of new interatomic potentials. Using … Continue reading
Posted in Molecular Dynamics
1 Comment
MOSCITO
Moscito is designed for condensed phase and gas phase MD simulations of molecular aggregates. Standard molecular mechanics force-fields such as AMBER, OPLS, CHARMM and GROMOS can be employed. Simulations can be carried out in different ensembles such as NVE, NVT … Continue reading
Posted in Molecular Dynamics
Leave a comment
Fungimol
Fungimol is an extensible system for designing atomic-scale objects. The intent is to eventually extend it to be a useful system for doing molecular nanotechnology design work. At the moment it’s a PDB file viewer and Buckminsterfullerine editor. Find Fungimol … Continue reading
Posted in Theoretical and Computational
Leave a comment
CACTVS
CACTVS is a distributed client/server system for the computation, management, analysis and visualisation of chemical information of any, even dynamically and ad-hoc defined type. Find CACTVS at: http://www2.chemie.uni-erlangen.de/software/cactvs/index.html
Posted in Theoretical and Computational
Leave a comment
NAB
The NAB molecular manipulation language – a computer language (specified through lex and yacc) that allows nucleic acid structures to be described in a hierarchical fashion, using a language similar to C or awk, but designed especially for the manipulatio … Continue reading
Posted in Theoretical and Computational
Leave a comment