MD_mcx45_vandenyje_ikrautas_isoflurane/notes

#ikrauti HIS turetu nustumti/pritraukti isoflurane ^_^
#kur rugstys veikia jos kitaip, su NH4Cl nesusije!
#jau seniau padaryta kaip jie didina kilpu judruma
#isoflurane prep:
#R ir S pervadinti skirtingai, kad butu
export PATH=$PATH:/home/vytautas/bin/amber16/bin/ && export AMBERHOME=/home/vytautas/bin/amber16
acpype -i isofluraneR.pdb
acpype -i isofluraneS.pdb
#atomtypes antra iskomentuoti, nes tas pats

gmx pdb2gmx -f Cx45_model_01pus.pdb -o mcx45_processed.gro -ff amber99sb-ildn -water spce -ignh -his
#AMBER99SB-ILDN
#pirmiau HD1 nebuvo dabar 66
#104HIS    HD1 tik buvo.
gmx editconf -f mcx45_processed.gro -o mcx45_newbox.gro -c -d 1 -bt cubic
#new box volume  :3332.52               (nm^3)
#furane konc.: 3 mM str.
#furane vnt. paskaiciuot:
#kazkur 6 vnt. turetu ciua plaukioti tada (3 R ir 3 S)
#http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
gmx insert-molecules -nmol 3 -f mcx45_newbox.gro -ci isofluraneR.acpype/isofluraneR_GMX.gro -o mcx45_isofR.gro
gmx insert-molecules -nmol 3 -f mcx45_isofR.gro -ci isofluraneS.acpype/isofluraneS_GMX.gro -o mcx45_isof.gro

gmx solvate -cp mcx45_isof.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
#42 vnt. CL reikes.
gmx genion -s ions.tpr -o mcx45_solv_ions.gro -p topol.top -nn 42
#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 md_0_1.gro -t md_0_1.cpt -p topol.top -o md_0_p.tpr
/home/vytautas/bin/plumed/gromacs-2016.1/bin/gmx mdrun -quiet -v -deffnm md_0_p -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 -res