gmx genconf -f dppc.gro -o b_64.gro -nbox 4 4 4
editconf -f dppc.gro -o dppc.pdb
editconf -f b_64.gro -o b_64.pdb
import __main__
__main__.pymol_argv = [ 'pymol', '-x' ]
import pymol
pymol.finish_launching()
from pymol import cmd
from IPython.display import Image
cmd.do('''
load dppc.pdb
bg_color white
ray
png dppc.png
delete dppc
load b_64.pdb
orient b_64
ray
png b_64.png
delete b_64
load b_s.pdb
orient b_s
ray
png b_s.png
delete b_s
load b_pr.pdb
orient b_pr
ray
png b_pr.png
delete b_pr
''')
Image(filename='dppc.png')
Image(filename='b_64.png')
gmx editconf -f b_64.gro -o b_ec -d 0.5
gmx grompp -f em -c b_ec -p b -o b_em -maxwarn 2
gmx mdrun -deffnm b_em -v
gmx solvate -cp b_em -p b -cs spc216 -o b_s
gmx grompp -f pr -c b_s -p b -o b_pr -maxwarn 1
gmx mdrun -deffnm b_pr -v
Image(filename='b_s.png')
Image(filename='b_pr.png')
from IPython.core.display import display, HTML
html_custom = '<h4>Файлы, полученные выше, лежат в этой <a href="https://kodomo.fbb.msu.ru/~agayeva_zarifa/term8/pr11_files">папке</a>.</h4>'
display(HTML(html_custom))
gmx grompp -f md -c b_pr -p b -o b_md -maxwarn 1
sbatch -N1 --ntasks-per-node=1 -e error.log -o output.log -t 5 -p test ompi /opt/ccoe/gromacs-2020.3-gcc-cuda/bin/gmx mdrun -deffnm b_md -v