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