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