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Week 7

Analysis of An extended simulation of BPTI (or if you have another system to study). Week 7. Weekly Plan. Monday: analsys w/ VMD scripts Load trajectory, rmsd, strip water Radial distribution Diffusion Wednesday: Making these work for you Friday: presentations. Simple VMD scripts.

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Week 7

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  1. Analysis of An extended simulation of BPTI (or if you have another system to study) Week 7

  2. Weekly Plan • Monday: analsys w/ VMD scripts • Load trajectory, rmsd, strip water • Radial distribution • Diffusion • Wednesday: • Making these work for you • Friday: presentations

  3. Simple VMD scripts

  4. Load trajectories as scripts load-dcds.vmd rmsd.tcl see namd-tutorial-unix sect 1.8.1 pg33 Rmsd-5.tcl see namd-tutorial-unix pg 35 residue_rmsd.tcl see pg 35 This one takes some time

  5. Maxwell-Boltzmann KE & T Analysis Energy.tcl Mixed with xmgrace analysis See pages 40-43 Temperature by “hand” See pg 48

  6. RMSD analysis N is the number of atoms being compared. Nt is the number of time steps being used in the calculation. r(tj) is the position of  atom at time t and <r> is the average value of the position of atom . The RMSD should converge if the atoms are not “flowing” but rather fluctuating around some position.

  7. Boltzman H-function from Velocities in NVT (canonical) Fraction of atoms with velocity between v and v + dv For any component For any function A that depends on velocities (e.g. K.E.) Boltzmann's H-function as measure equilibration. Hx is negative and should decrease in time to by f(vx)dvx above “Molecular Dynamics Simulations, Elem.Methods”, J.M.Haile, Chap 2.7

  8. Diffusion Green-Kubo expression for integrated velocity autocorrelation function. (see McQuarrie Stat. Mechanics) Or the usual expression

  9. BPTI Simulation Study on LONI 1) system: 150mM salt ; 10A shell all directions 2) the simulation a) minimize and equilibrate b) benchmarks 1-32 CPU c) NTP dynamics for 10ns on 16CPU 3) Analysis a) show that system equilibrated to target T & P b) RMSD analysis of system protein c) Diffusion of water using velocities d) Radial Distribution analysis waters …. more

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