GROMACS 2020 notes

#su Chimera istraukti SAM pdb (SAM.pdb).
#tik chain A ir SAM atskiruose failuose ir dockprep
#tada su Chimera atgal i pdb fix
export PATH=$PATH:/home/vytautas/bin/amber16/bin/ && export AMBERHOME=/home/vytautas/bin/amber16
#Chimeros amber:
#export PATH=$PATH:/home/vytautas/.local/UCSF-Chimera64-1.14/bin/amber18/bin/ && export AMBERHOME=/home/vytautas/.local/UCSF-Chimera64-1.14/bin/amber18
acpype -i SAM_fix.pdb -n 1

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

#pymol states buvo trys imta 1, nes tinka seka.
gmx pdb2gmx -f 6W4H_A_fix.pdb -o 6W4H_processed.gro -water spce -ignh

#SAM_fix.acpype/SAM_fix_GMX.gro
#i 6W4H_processed.gro gala ir virsuj nr. prideti atomu sk.
#i topol.top pradzioj:
#include "SAM_fix.acpype/SAM_fix_GMX.itp"
#O gale:
#SAM_fix 1

#box:
gmx editconf -f 6W4H_processed.gro -o 6W4H_newbox.gro -c -d 1.0 -bt cubic

#vanduo:
gmx solvate -cp 6W4H_newbox.gro -cs spc216.gro -o 6W4H_solv.gro -p topol.top

#jonai:
#wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/ions.mdp :(
#cp ~/MD_Cx43_lycopene_DOCK_2/*.mdp .
gmx grompp -f ions.mdp -c 6W4H_solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o 6W4H_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 6W4H_solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -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 -r em.gro -p topol.top -o nvt.tpr
gmx mdrun -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 -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
gmx mdrun -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 -deffnm md_0_1

#testi nuo checkpointo:
gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt

#rez i pdb:
gmx trjconv -f md_0_1.trr -s md_0_1.gro -skip 10 -o md_0_1.pdb
#kisenes ner :\
#tiksliau paziureti:
#nstxout         = 50           ; save coordinates
gmx trjconv -f em.trr -s em.gro -o em.pdb
PyMOL>cealign 6w4h__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

#energija:
gmx energy -f md_0_1.edr -o md_ener.xvg
#rms:
gmx rms -s md_0_1.tpr -f md_0_1.xtc