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- gmx pdb2gmx -f Cx45_model_01pus.pdb -o mcx45_processed.gro -ff amber99sb-ildn -water spce -ignh
- #AMBER99SB-ILDN
- gmx editconf -f mcx45_processed.gro -o mcx45_newbox.gro -c -d 1 -bt cubic
- gmx solvate -cp mcx45_newbox.gro -cs spc216.gro -o mcx45_solv.gro -p topol.top
- # npt/nvt buvo daug save pratrinta.
- # o kitkas pagal
- # http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/
- gmx grompp -f ions.mdp -c mcx45_solv.gro -p topol.top -o ions.tpr
- #48 vnt. NA reikes.
- gmx genion -s ions.tpr -o mcx45_solv_ions.gro -p topol.top -np 24
- #minim:
- gmx grompp -quiet -f minim.mdp -c mcx45_solv_ions.gro -p topol.top -o em.tpr
- gmx mdrun -quiet -v -deffnm em
- #nvt:
- gmx grompp -quiet -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
- gmx mdrun -quiet -v -deffnm nvt
- #npt:
- gmx grompp -quiet -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
- gmx mdrun -quiet -v -deffnm npt
- #md:
- gmx grompp -quiet -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
- gmx mdrun -quiet -v -deffnm md_0_1
- gmx trjconv -quiet -pbc mol -f md_0_1.trr -fit trans -s md_0_1.tpr -o md_0_1.pdb
- #plumed md:
- /home/vytautas/bin/plumed/gromacs-2016.1/bin/gmx grompp -quiet -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
- /home/vytautas/bin/plumed/gromacs-2016.1/bin/gmx mdrun -quiet -v -deffnm md_0_1 -plumed plumed.dat
- #rmsd
- gmx rms -s npt.gro -f md_0_1.xtc
- gmx rmsf -s md_0_1.tpr -f md_0_1.xtc
- #cia buvo neutralus HIS
- #paskui dar leisti su ikrautais visais HIS
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