MD_notes_20180913

Pasirinktas:
 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)

#python2.7 rename_pdb.py 6 Cx43_full_hexa.pdb

#imamas puskanalis sumodeliuotas su SWISS-MODEL, QUARK:
gmx pdb2gmx -f Cx43_full_hexa.pdb -o Cx43_processed.gro -water spce -ignh

#box:
gmx editconf -f Cx43_processed.gro -o Cx43_newbox.gro -c -d 1.0 -bt cubic

#vanduo:
gmx solvate -cp Cx43_newbox.gro -cs spc216.gro -o Cx43_solv.gro -p topol.top

#jonai:
#wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/ions.mdp
#gmx grompp -f ions.mdp -c Cx43_solv.gro -p topol.top -o ions.tpr
#gmx genion -s ions.tpr -o Cx43_solv_K.gro -p topol.top -np 1 -pname K

#neutralizuoti ir minim pakeista:
gmx grompp -f ions.mdp -c Cx43_solv.gro -p topol.top -o ions.tpr -maxwarn 1
gmx genion -s ions.tpr -o Cx43_solv_ions.gro -p topol.top -neutral

#minimizacija:
wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
gmx grompp -f minim.mdp -c Cx43_solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -quiet -v -deffnm em

#Equilibration
wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/nvt.mdp
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
gmx mdrun -quiet -v -deffnm nvt

#Equilibration 2
wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/npt.mdp
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
gmx mdrun -quiet -v -deffnm npt

#MD run:
#wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
gmx mdrun -v -deffnm md_0_1

#nereiks situ: rez i pdb:
#gmx trjconv -f md_0_1.trr -s md_0_1.gro -skip 10 -o md_0_1.pdb
#gmx trjconv -f em.trr -s em.gro -o em.pdb
#PyMOL>cealign Cx43__state01, em
#PyMOL>zoom hexanol_kisenej
#gmx trjconv -f md_0_1.trr -fit rot+trans -s md_0_1.gro -skip 10 -o md_0_1.pdb
#atstumai tarp CIS 92 sieros ir CIS 264 sieros grafiku:
#; Paskaiciuot atstumus nuo laiko:
#;
#; Use "gmx distance -n index.ndx -f md_0_1.trr -s md_0_1.tpr -oav -oall"
#; with index file write in this way:
#;
#[SG_92 - SG_1203]
#
#1477 19736
#paskui:
#xmgrace dist.xvg

#grep " 87PRO     CA" npt.gro

#/home/farmacija/bin/plumed/gromacs-2018.3/bin/gmx grompp -quiet -f md.mdp -c npt.gro -p topol.top -o md_0_1.tpr
#/home/farmacija/bin/plumed/gromacs-2018.3/bin/gmx mdrun -quiet -v -ntomp 10 -deffnm md_0_1 -plumed plumed_sutempti.dat

/home/farmacija/bin/plumed/gromacs-2018.3/bin/gmx grompp -quiet -f md.mdp -c md_0_1.gro -p topol.top -o md_0_2.tpr
/home/farmacija/bin/plumed/gromacs-2018.3/bin/gmx mdrun -quiet -v -deffnm md_0_2 -plumed galai_metadinamika.dat

#plot:
#awk -F ' ' '{print $1, " ", $2}' COLVAR > COLVAR_t_ang
#xmgrace COLVAR_t_ang
#
##plot:
gnuplot> p "COLVAR_K+_pratempti" u 1:7 w lp,\
#>"COLVAR_K+_pratempti" u 1:14 w lp,\
>"COLVAR_K+_pratempti" u 1:13 w lp;

#pan. jau buvo bet biski daugiau KAPPA gal.
gmx energy -quiet -f md_0_1.edr
#50  Coul-SR:K-Protein
#iseina paskui energy.xvg failas
#
#gro i pdb:
gmx trjconv -f md_0_1.gro -s md_0_1.gro -o md_0_1.pdb
gmx trjconv -f md_0_2.trr -s md_0_2.gro -o md_0_2.pdb
#sum_hills su plumed:
/home/farmacija/bin/plumed/plumed-2.4.2/src/lib/plumed sum_hills --hills HILLS