1 / 8

Monday of Week 3

Monday of Week 3. Monday: force fields and Verlet integration Building a bpti simulation Wed – Friday: Making water box Running namd and analysis. General Workflow in MD. The BPTI Sims. simulation in vacuum: test simulation set up configuration files ; test stuff

inigo
Download Presentation

Monday of Week 3

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. Monday of Week 3 • Monday: • force fields and Verlet integration • Building a bpti simulation • Wed – Friday: • Making water box • Running namd and analysis

  2. General Workflow in MD

  3. The BPTI Sims • simulation in vacuum: test simulation • set up configuration files ; test stuff • minimize the xray structure esp. if missing parts • solvate the system: real simulation • start with minimized structure from previous • add waters and ions • minimize • equilibration • simulate

  4. Organization of BPTI Sims • /scratch00/BMEN662/bpti • bld: INITIAL INPUTS • topology; params; • psfgen info and scripts • xray structures; solvated systems etc.. • vac-sim: Simulation of Initial Inputs • inputs: conf, ../bld/[ psf, pdb] ../bld/parm • outpus: dcd, vel, out, coor, xsc, xst • solv-sim: Solvated simulation • inputs: confs, ../bld/[psf,pdb] ../bld/parm • outputs: dcd, vel, out, coor, xsc, xst • min-eq: these feed the next step • dyn

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

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

  7. Maxwell-Boltzman Distrib. • 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

  8. 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

More Related