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Norma
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Table of Contents
First-time users
Molecular dynamics
PyMOL
First-time users
What is a cluster ?
What is a Beowulf cluster ?
Approaching Norma
Rules of engagement
Submitting a NAMD job
Submitting a CNS job
Submitting a vina (autodock) job
Submitting a generic serial job (eg. CCP4)
Submitting a MPI (parallel) job
Backup, backup, backup
Molecular dynamics
Nefeli's
molecular dynamics tutorials.
^{1)}
Nefeli's
molecular dynamics analyses.
Using the OPLS-AA forcefield
Using the CHARMM forcefield with the CMAP correction
Using the AMBER forcefield
AMBER99SB-ILDN, TIP4P-Ew and NAMD
Using the AMBER12SB and AMBER14SB forcefield
Using methanol, TFE or water/TFE mixtures as solvents in folding simulations
Estimating minimal PBC box for a folding simulation
Using a 4fs timestep through Hydrogen Mass Repartitioning
Calculation of a principal component's cosine content
Calculation of interaction energies using NAMD
Preparation of 'distance vs. Rg' plots
Preparation of 'Energy vs. Surface area' plots
Positional autocorrelation function
MD and NMR, calculation of NOEs
MD and NMR, calculation of J-couplings
MD and NMR, calculation of chemical shifts
Calculation of RMSD matrices and cluster analysis
Comparison of carma-derived clusters and RMSD (crossDCD) matrices
High dimensionality PCA-based cluster analysis using K-means
High dimensionality PCA-based cluster analysis using a Bayesian approach
Distance-matrix-based clustering of principal components (dPCA or cPCA)
Preparation of diagrams based on native contacts (Q, Qs, q)
Adaptive tempering : (T vs Q) and other diagrams
Adaptive tempering : (Secondary structure vs T) diagrams
Attempts to quantify how different (or similar) two trajectories are
Torsion-RMSD, calculation and applications
R, MDS and friends
PyMOL
HD movies using PyMOL
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Ignore the stuff about opemosix and job submission. Remember that these were made during the NAMD 2.5 era
research/howto.txt · Last modified: 2018/07/20 21:07 (external edit)