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MMTSB/CTBP Summer Workshop Result of MSD calculation ”pept500.msd” time (ps) MSD (Å 2 ) 0.00000E+00 0.00000E+00 0.50000E+01 0.16341E+02 0.10000E+02 0.32182E+02 0.15000E+02 0.47965E+02 0.20000E+02 0.63677E+02 0.25000E+02 0.79330E+02 0.30000E+02 0.94947E+02 0.35000E+02 0.11055E+03 0.40000E+02 0.12612E+03 0.45000E+02 0.14158E+03 ] MSD [Å 2 300 250 200 150 100 50 0 0 20 40 60 80 100 Time [ps] D=( MSD(45)-MSD(5) )/(6* (45-5) )= (140-16)/240=0.53 [Å 2 /ps]=5.3 10 -9 [m 2 /s] © Lennart Nilsson , 2006.
MMTSB/CTBP Summer Workshop Clustering structures Similar Sequence Similar Structure ? Known structures RMSD The Protein Universe with protein “families” © 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 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: MMTSB/CTBP Summer Workshop MSD calc
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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