1 / 9

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.

vivek
Download Presentation

Week 7

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related