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Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) [1] is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model (not to be confused with CHARMM). It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms). [2]
Software platform, allows organizations to integrate, analyze, and share complex biomedical data Linux, macOS, Windows: Apache: LabKey Software Foundation LAMMPS: Molecular dynamics program written in C++: Linux, macOS, Windows: Apache: Sandia National Laboratories. mothur: Software for analysis of 16S rRNA gene amplicon sequence data Linux ...
Free open source MIT: OpenMM: Orac: No No Yes Yes No Yes No Yes No Molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomic level Free open source: Orac download page: NAMD + VMD: Yes Yes Yes Yes No Yes I Yes Yes Fast, parallel MD, CUDA Proprietary, free academic use, source code Beckman ...
Other simulation methods (such as replica exchange) are supported through a plug-in-based infrastructure, which also allows users to develop their own simulation algorithms and models. Desmond is also available in a graphics processing unit (GPU) accelerated version that is about 60-80 times faster than the central processing unit (CPU) version.
Meiosis generates genetic variation in the diploid cell, in part by the exchange of genetic information between the pairs of chromosomes after they align (recombination). Thus, on this view, [28] an advantage of meiosis is that it facilitates the generation of genomic diversity among progeny, allowing adaptation to adverse changes in the ...
This is a category of articles relating to software which can be freely used, copied, studied, modified, and redistributed by everyone that obtains a copy: "free software" or "open source software". Typically, this means software which is distributed with a free software license , and whose source code is available to anyone who receives a copy ...
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Open source software provides a platform for computational biology where everyone can access and benefit from software developed in research. PLOS cites [citation needed] four main reasons for the use of open source software: Reproducibility: This allows for researchers to use the exact methods used to calculate the relations between biological ...