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MMTSB/CTBP Summer Workshop COOR ANALysis, cont´d g(r) for water oxygens wrt backbone amide hydrogens When several solute atoms are specified as the site their average position will be used as the reference position if MULTi is not present open unit 21 read unform name pept500.cor open unit 31 write form name pept500.gonh coor anal select type oh2 end - site select type HN end multi – firstu 21 nunit 1 skip 500 - isdist 31 mgn 100 dr 0.1 rsph 999.9 Several types of analysis (with some exceptions) may be combined in a single ”coor analysis” command. © Lennart Nilsson , 2006.
MMTSB/CTBP Summer Workshop Water g OO (r) SPC/E SPC TIP3P © Lennart Nilsson , 2006.
Page 1 and 2: MMTSB/CTBP Summer Workshop CHARMM A
Page 3 and 4: MMTSB/CTBP Summer Workshop Basic an
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: MMTSB/CTBP Summer Workshop Geometry
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

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