Nonstandard Topology Files
Mg2+ in charged RNA: Ryan Hayes et al.
Two tarred directories are provided. The first, ARibo_Mg3.2e-5_MCK20.tar, contains Gromacs input files to simulate the Adenine Riboswitch in 50 mM KCl and 0.032 mM MgCl2. Running the file ./run.tcsh will create a .tpr file an submit it to mdrun. Because Gromacs does not analytically include Debye Huckel interactions, Debye Huckel interactions are included in tables. The forces in these tables depend on both the screening length and the Manning condensed K, and should be treated with care.
The second tarred directory, GenerateFiles.tar, contains a script and data files allowing you to generate your own charged SBM of RNA. Runfiles and Debye Huckel tables are generated automatically, provided that the values of MCK the manning condensed KCl, and Gamma_EXP, an initial guess for the excess Mg (or Preferential interaction coefficient of Mg) are sensible. Values for Gamma_EXP can be calculated from simulation, and corrected iteratively, choosing the correct value for MCK is still an open topic of research. At least 200 Mg ions are added to the system so there will be a good bulk population of ions. Currently, only top files containing single chains can be generated with the script.