CHARMM Analysis Tools

Recommendations

Info

MMTSB/CTBP Summer Workshop Overview • Basic analysis issues • Main <strong>CHARMM</strong> analysis modules • Single structure • Trajectory • Examples: Solvent, hydrogen bonding, clustering © Lennart Nilsson , 2006.
MMTSB/CTBP Summer Workshop Basic analysis issues • What do I want to know from my simulation? How can this help with my scientific problem? HAVE TO BE ADDRESSED EARLY ! ! ! • A single number (energy value,…) – convergence? • Properties of a single structure – representative? • Properties of a population – how many? • Time-dependence – time-scales? • (almost) All analysis in <strong>CHARMM</strong> is done by postprocessing a coordinate file or a trajectory © Lennart Nilsson , 2006.
Page 1: MMTSB/CTBP Summer Workshop CHARMM A
Page 5 and 6: MMTSB/CTBP Summer Workshop Single s
Page 7 and 8: MMTSB/CTBP Summer Workshop Energy e
Page 9 and 10: MMTSB/CTBP Summer Workshop Hydrogen
Page 11 and 12: MMTSB/CTBP Summer Workshop Hydrogen
Page 13 and 14: Finding hydrogen bonds in a single
Page 15 and 16: MMTSB/CTBP Summer Workshop Protein
Page 17 and 18: Snapshots can be anlyzed in a loop
Page 19 and 20: Hydrogen bonds from a trajectory co
Page 21 and 22: MMTSB/CTBP Summer Workshop Solvent
Page 23 and 24: MMTSB/CTBP Summer Workshop Geometry
Page 25 and 26: MMTSB/CTBP Summer Workshop Water g
Page 27 and 28: Hydration number / 3D histogram MMT
Page 29 and 30: MMTSB/CTBP Summer Workshop MSD calc
Page 31 and 32: MMTSB/CTBP Summer Workshop Clusteri
Page 33 and 34: Clustering with CHARMM, example cor
Page 35 and 36: MMTSB/CTBP Summer Workshop q 1.5 1.
Page 37 and 38: Example time-dependent fluorescence
Page 39 and 40: MMTSB/CTBP Summer Workshop Example
Page 41 and 42: MMTSB/CTBP Summer Workshop www.char

CHARMM Analysis Tools

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?