paskui dar leisti su ikrautais visais HIS

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