Amber 10 Tutorial Minimization in Sander Minimization It
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 Amber 10 Manual. pdf. These 2 pages show the syntax of how to run the sander command function. • All page numbers here will refer to the “Amber 10 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/ H 20 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. 0 E-4, ntb=1, cut=12. 0, igb=0, / EOF echo 'begin bnr minimization' >> timer. date >> timer. dat bnra=/home/saguaro/Quickgo/amber 10 tutorial sander -i min. in -o min. out -p $bnra/bnrwh 2 o. top -c $bnra/bnrwh 2 o. 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 i. CRD 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. 0 E-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 i. PBC 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 a lot of gb types to choose from
Minimization • An example run of this can be found on saguaro@dnaseq in the directory ~/Quickgo/amber 10 tutorial/bnr. MD/minimize/
- Slides: 6