MBG wiki
|
RecentChanges
|
Blog
|
2024-05-06
|
2024-05-05
Editing Molecular dynamics studies of HrcQb
This project is in collaboration with IMBB, FORTH. Person responsible : Dr Vasiliki E. Fadouloglou (fadoulog@imbb.forth.gr) * Getting started **[[Force field]] **[[Create the files needed]] * Simulation of native HrcQb **[[heating-up NAMD script]] **[[equilibration NAMD script]] **[[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 ** [[Heating-up NAMD script for 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]]
Summary:
This change is a minor edit.
Username:
Replace this text with a file.