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Amber 10 Tutorial. Minimization in Sander. 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”.

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amber 10 tutorial

Amber 10 Tutorial

Minimization in Sander

minimization
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”
minimization sh
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

min in
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.
min in1
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
minimization1
Minimization
  • An example run of this can be found on [email protected] in the directory ~/Quickgo/amber10tutorial/bnrMD/minimize/
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