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Wednesday of Week 3

Wednesday of Week 3. Monday: force fields and Verlet integration Building a bpti simulation Wednesday: Review of sims setup on dropbox Water,salt-water,bpti Running namd and analysis Friday: Student reports on progress. Review. Organization of Sims Directory. bin bpti salt-water

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Wednesday of Week 3

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  1. Wednesday of Week 3 • Monday: • force fields and Verlet integration • Building a bpti simulation • Wednesday: • Review of sims setup on dropbox • Water,salt-water,bpti • Running namd and analysis • Friday: • Student reports on progress

  2. Review

  3. Organization of Sims Directory bin bpti salt-water water

  4. BIN Some sample scripts for reference The tcl scripts can be run from within vmd once a molecule and dynamics have been loaded or as a command line in unix e.g. vmd -psf bpti.psf -pdb bpti.pdb -dcd dyn1.dcd -e some.tcl The other scripts are binary shell scripts that work in unix

  5. Water SCRIPTS TO RUN FOR SIM AND ANALY: 01-make-water.vmd: makes a box of water 02-min-eq.PBC.namd: does min and equilib of the box 03-dyn1.namd: runs a namd sim of the box 04-analy.tcsh: some simple analysis scripts • kineticenergy.tcl ******** INPUT and OUTPU all appears in Analy/ kineticenergy.tcl dumps here IN/ OUT/

  6. Give them a walk thru of water vmd -e 01-make-water.vmd namd2 02-min-eq.PBC.namd > OUT/min-eq.out namd2 03-dyn1.namd > OUT/dyn1.out Show how to load log file in vmd and view it

  7. salt-water SCRIPTS TO RUN FOR SIM AND ANALY: 01-make-water.vmd: makes a box of water 01-a.vmd: manually make “ioninzed” system 02-min-eq.PBC.namd: does min and equilib of the box 03-dyn1.namd: runs a namd sim of the box 03-dyn1.ntp.namd: runs with different options 04-analy.txt: some simple analysis scripts • kineticenergy.tcl ******** INPUT and OUTPU all appears in Analy/ kineticenergy.tcl dumps here IN/ OUT/

  8. Give them a walk thru of salt-water Same general build recipe Use psfsgen to make box of water then use vmd -psf water.psf -pdb water.pdb use the “Extensions->modeling-> addions” tools Note sims use “ionized” for inputs The PBC files demonstrate different options you can create these with VMD, but I prefer to run in a shell for greater control (e.g. # cpu)

  9. bpti • SCRIPTS TO RUN FOR SIM AND ANALY: • 01-make-bpti-psfgen.vmd • 02-make-bpti-solvated.vmd • Different PBC • 03-min-eq.noPBC.namd • 03-min-eq.PBC.namd • Different Dynamics • 04-dyn1.namd • 04-dyn1.npt.namd • 04-dyn1.nve.namd • 04-dyn1.nvt.namd • 04-dyn2.namd • Some analysis: • 05-load-all-nofit.vmd • 05-load-all-sims.vmd

  10. Bpti-sims walk thru Building is a multi-step process Build up system , add water then do min-eq and dyn Min-eq with and without PBC (periodic boundaries are given for completeness) Many different run options are given for 04-dyn Scripts to load up all sims are in 05-load Run these as “vmd -e 05-load-all-sims.vmd”

  11. Analysis

  12. NAMD plot • VMD has a rudimentary plotting tool ) • copy simulation “.out” file to local system • start VMD • Extensions -> Namd Plot : Log File -> “.out” • Select Energy and look at plots • namdenr (extract data from .out file) • plot with “your favorite plotter” • xmgrace thru xterm • excell

  13. Maxwell-Boltzman Distrib from KE. • load psf and VELOCITY FILE • copy the energy.tcl script from bpti/analy • vmd -dispdev none -psf bpti.solv.psf -dcd -e energy.tcl • xmgrace -nxy energy.dat • Data->Transformations -> Histograms • normalize and start,stop, #bins • Data->Transformations-> Nonlinear Curve: y = (2/ sqrt(Pi * a0 ^ $3 )) * sqrt(x) * exp (-x / a0) ao corresponds to kT in kcal/mo at 300K this is ~ 0.6 kb = 0.00198657 kcal/mol-K

  14. 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

  15. RMSD If the RMSD does not converge to some point then the system has not equilibrated, assuming you only calc. for protein

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

  17. Backcalculating a Force Constant • If equilibrated then equipartition holds • Each oscillator has 1/2kT of energy so for all bonds which have 1/2Ko(R-Ro)^2 then nbonds/2kT = 1/2Ko<R-R0>^2 or <R-Ro>^2*kT/nbonds = Ko of course must use the same types of bonds

  18. Some Exercises to Consider 0) simple plots of Temp, Press, Volume and other quantities from VMD to assess the simulations. 1) simple plots of RMSD for water, ions and protein how should these behave? ABOVE CAN BE DONE BY FRIDAY below should be proposed in more detail on Friday. 2) vary “timestep” in 04-dyn1.nve.namd and see if in fact total Energy is constant. Since Verlet is O(dt^4) can you demonstrate this by using different values for time step? What's largest dt you can use and have energy conserved? 3)check g(r) using vmd “extensions” for water and/or salt-water and see if values are correct How long does it take for g(r) to “equlibrate” 4) monitor the structure of bpti during different simulation conditions. Specifically if you compare RMS of bpti during NVE, NVT, and NTP runs it differs is this just a sampling thing or is something “wrong” 5)Are values of diffusion of water correct in various simulations? How does the “langevin damping” value in NPT sims alter diffusion values?

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