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Quick Guide to Minimization in Amber 10 Using Sander

This tutorial provides essential instructions for performing minimization in Amber 10 with the Sander command function. Key syntax and parameters, including the maximum number of cycles, minimization type, and boundary conditions, are explained in detail. You'll learn to configure your minimization run for optimal results, with specific focus on settings like `maxcyc`, `imin`, `ntx`, and others. Additionally, this guide offers insights into practical examples and best practices for running molecular simulations effectively.

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Quick Guide to Minimization in Amber 10 Using Sander

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  1. Amber 10 Tutorial Minimization in Sander

  2. Minimization • It is important to do a quick read of pg. 21 and the start of pg 22 of Amber10 Manual.pdf. These 2 pages show the syntax of how to run the sander command function. • All page numbers here will refer to the “Amber10 Manual.pdf”

  3. minimization.sh The code below is the code to run a minimization in sander. It will be described in detail in the next few slides. #Running minimization for lys w/ H20 cat << EOF > min.in #5000 steps of minimization &cntrl maxcyc=5000,imin=1,ntx=1,ntwx=0,ntwv=0,ntwe=1, ncyc=20,ntmin=1,drms=1.0E-4,ntb=1,cut=12.0, igb=0, / EOF echo 'begin bnr minimization' >> timer.dat date >> timer.dat bnra=/home/saguaro/Quickgo/amber10tutorial sander -imin.in -o min.out -p $bnra/bnrwh2o.top -c $bnra/bnrwh2o.crd -r min.rst -e min.ene date >> timer.dat echo 'end bnr minimization' >> timer.dat

  4. Min.in • maxcyc = 5000 pg 27 • maximum number of cycles the minimizations will run before it stops • like NSTEP in saguaro • imin = 1 pg 23 • 1 means do minimization and no molecular dynamics • same as imin in saguaro except an analysis option, imin = 5 • ntx = 1 pg 24 • reads in formatted (i.e. not binary) coordinates without velocites • similar to iCRD in saguaro, but NOT the same. • ntwx,ntwv,ntwe = # pg 25,26 • these denote the number (#) of steps between writing the positions (x), velocities (v), or energies (e) of the run. • minimization doesn’t write any of these out.

  5. Min.in • ntmin = 1 pg 27 • applies the stepest descent algorithm to the minimization run for ncyc then switches to the conjugate gradient. • ncyc = 20 pg 27 • 20 steps before the run switches to conjugate gradient. • drms = 1.0E-4 pg 27 • the run will stop when the root-mean-square of the coordinates of the gradient is less than this value. Units are in kcal/(mol-angstrom) • ntb = 1 pg 35 • this is periodic boundary conditions (constant volume) • this is the same as iPBC in saguaro • cut = 12.0 pg 35 • non-bonded cutoff in angstroms. I should have used 8 here because this is explicit water. • igb = 0 pg 36 & 54 • 0 turns off generalized born. Unlike saguaro there are a lot of gb types to choose from

  6. Minimization • An example run of this can be found on saguaro@dnaseq in the directory ~/Quickgo/amber10tutorial/bnrMD/minimize/

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