Nonstandard Topology Files

Non-specific magnesium-RNA interaction model with generalized Manning model of KCl: Hayes et al. (2015) PRL

NOTE: This study is completely separate from SMOG in that it runs with its own self-created MD engine. The interactions needed were difficult to include into the GROMACS source code.

A tarred directory containing an md engine and example files for several RNA systems are linked below. The md engine allows the implicit KCl condensation to vary with time and RNA conformation, which is not straightforward to implement within gromacs. Standard top files for RNA output by the smog server may be used. The atom coordinates and charges are provided by a separate .xyzq file, rather than the .gro file provided by the smog server.

For details of the potential, please read and cite Hayes et al., PRL, 2015. For usage details see the enclosed README file.


  1. MD_RNAIONS.tar.gz

This resource is provided by the Center for Theoretical Biological Physics.
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