Molecular Dynamics

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Molecular modelling consists of a collection of theoretical techniques for studying the behaviour of molecules. Those techniques are frequently used in bio-informatics, where the structure and the dynamics of the molecules that make up living beings are investigated: proteins, DNA and RNA, biological membranes, etc.

These molecules are complex (several thousand atoms) and represent an important computational challenge. Simulating the properties of these molecules is a non-trivial problem that requires techniques for decomposing into domains to parallelize. These kinds of calculations usually require a lot of communication between compute nodes, and InfiniBand QDR connectivity is desirable to minimize the synchronization of processes.

Applications and libraries for molecular dynamics

Among the most common applications and software libraries used for molecular dynamics, several are installed on Calcul Québec supercomputers. Notably we have the following packages:

For a detailed list of installed versions on each server, please refer to the list of modules installed on each Calcul Québec server.

Strengths and weaknesses of the applications

To complete.

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