All atom molecular simulation toolkit.


Almsot 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.

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 will use the default algorithm, while Energy 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.



NMRbox Version Software Version
1.0.0 2.1.0,
2.0.0 2.1.0,
3.0.0 2.1.0,


  • Molecular Dynamics
  • Structure Refinement


ALMOST: an all atom molecular simulation toolkit for protein structure determination
Vendruscolo Michele, Sahakyan Aleksandr B, Cavalli Andrea, Fu Biao, Camilloni Carlo, Tartaglia Gian Gaetano, Paci Emanuele, Caflisch Amedeo,
Journal of computational chemistry. 2014; 35(14): 1101--1105