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MMTSB/CTBP Summer Workshop Hydration number Calculate number of solvent molecules within a specified distance of a site: ?NHYDRR - number of solvent molecules (residues) ?NHYDAR - number of solvent atoms ?NHYDAA - number of solvent atoms within RHYD of solute atoms (3 water molecules within RHYD of a 7-atom solute NHYDAA=63) Sets the <strong>CHARMM</strong> variables to the averages over the trajectory, and prints the values to the logfile; optionally also to a file every timestep. coor anal sele resn tip3 .and. type oh2 end - site sele resn asp .and. type od1 show end multi - firstu 21 nunit 1 skip 500 rhyd 3.0 NB! You need keyword MULTi if the solute (the SITE) has more than one atom. Use COOR ANAL IHIST to get a 3D distribution (histogram) © Lennart Nilsson , 2006.
Hydration number / 3D histogram MMTSB/CTBP Summer Workshop RHYD Grid for histogram NB! Have to use oriented and recentered trajectory © Lennart Nilsson , 2006.
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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: MMTSB/CTBP Summer Workshop Water g
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
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