1 / 6

Amber 10 Tutorial

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”.

chyna
Télécharger la présentation

Amber 10 Tutorial

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. 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/

More Related