about almost

almost - all atom molecular simulation toolkit - is a fast and flexible molecular modeling environment that provides powerful and efficient algorithms for molecular simulation, homology modeling, de novo design and ab-initio calculations.

Written in C++, almost has been specifically designed to be used as an application framework for the rapid development of Computational Biology Software, as Command Line Tool or as a 3D Interactive Modeling Environment.

>> RAD with libAlmost >> Built-in scripting language >> 3D Visualization Toolkit

almost provides an extremely high performance. Algorithms and data structures have been optimized to take advantage of vector instructions and multi-core technology of modern CPUs, using type and architecture template traits. So, Energy<double,CPUPlain> will use the default algorithm, while Energy<float,CPUPSSE> a specialization for CPUs with the SSE instruction set. Assembly innermost loops for the energy and force computations are provided for the most common architectures.

>> Benchmarks

examples

Below you will find few interactive examples of the usage of almost. Enter the PDB code of protein and submit to generate a set of input scripts to perform some basic tasks. Then, press on the run button to see the result or download the scripts to run them on your computer.

>> Run example

license

almost is free software, available under the GNU General Public License.

Help  |  Example
 
Compute the energy of the selected protein.
run
download scripts
Energy- minimize the selected protein.
run
download scripts
Run a short molecular dynamics simulation
run
download scripts
Run a short Monte Carlo simulation with the selected protein.
run
download scripts

Andrea Cavalli
Last modified: Tue Jul 22 01:42:49 CEST 2008

Copyright © 1999-2008 Andrea Cavalli