Molecular dynamics studies of HrcQb

> **[[equilibration graphs]]
> * Simulation of HrcQb-like FliN (tetramer)
> **[[heating-up NAMD script for FliN 4mer]]
> **[[equilibration NAMD script for FliN 4mer]]
> **[[equilibration graphs for FliN 4mer]]
> * Simulation of the AD HrcQb dimer

> *Simulation of the BC HrcQb dimer
> **[[heating-up NAMD script for BC 2mer]]
> **[[equilibration NAMD script for BC 2mer]]
> **[[equilibration graphs for BC 2mer]]
> *Simulation of native FliN (dimer)
> **[[heating-up NAMD script for FliN 2mer]]
> **[[equilibration NAMD script for FliN 2mer]]
> **[[equilibration graphs for FliN 2mer]]
> *Simulation of T40I-HrcQb
> **[[heating-up NAMD script for T40I]]
> **[[equilibration NAMD script for T40I]]
> **[[equilibration graphs for T40I]]
> *Simulation of T40Y-HrcQb
> **[[heating-up NAMD script for T40Y]]
> **[[equilibration NAMD script for T40Y]]
> **[[equilibration graphs for T40Y]]
> *Simulation of T40W-HrcQb
> **[[heating-up NAMD script for T40W]]
> **[[equilibration NAMD script for T40W]]
> **[[equilibration graphs for T40W]]
> *Simulation of I41W-HrcQb
> **[[heating-up NAMD script for I41W]]
> **[[equilibration NAMD script for I41W]]
> **[[equilibration graphs for I41W]]
> *Comparative analysis
> **[[Ca-rmsd as a function of frame. Alignment based on 4mer]]
> **[[Ca-rmsd as a function of frame. Alignment based on 2mer]]
> **[[Average rmsd for each residue]]
> **[[Radius of gyration]]