Hi :-)
Following Tutorial assumes you have GROMACS 2018 installed and working in a directory with input PDB file named as protein.pdb
Using this you will run Temperature - Pressure Equilibration and Final production run on 10 cores.
GROMACS-2018
1. Converting PDB input to GROMACS compatible file.
gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce
2. Making a Box to make a boundary for box for simulation.
gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
3. Adding water molecule to the system.
gmx solvate -cp protein_newbox.gro -cs spc216.gro -o protein_solv.gro -p topol.top
4. Generating .tpr file; get ions.mdp here
gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr
5. Adding Ions to neutralised the system.
gmx genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1
6. Generating .tpr file; get minim.mdp here
gmx grompp -f minim.mdp -c protein_solv_ions.gro -p topol.top -o em.tpr
7. Running Energy Minimization to re-arrange ions.
gmx mdrun -v -deffnm em
8. Plotting Potential of the system.
gmx energy -f em.edr -o potential.xvg
9. Generating .tpr file; get nvt.mdp here
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
10. Running Temperature Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm nvt
11. Plotting Temperature of the system.
gmx energy -f nvt.edr -o temperature.xvg
12. Generating .tpr file; get npt.mdp here
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
13. Running Pressure Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm npt
14. Plotting Pressure of the system.
gmx energy -f npt.edr -o pressure.xvg
15. Plotting Density of the system.
gmx energy -f npt.edr -o density.xvg
16. Generating .tpr file; get md.mdp here
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
17. Running MD simulation.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm md_0_1
Please note -: It is just a tutorial for simplification of work flow detailed md tutorials can be found at http://www.mdtutorials.com/
Following Tutorial assumes you have GROMACS 2018 installed and working in a directory with input PDB file named as protein.pdb
Using this you will run Temperature - Pressure Equilibration and Final production run on 10 cores.
GROMACS-2018
1. Converting PDB input to GROMACS compatible file.
gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce
2. Making a Box to make a boundary for box for simulation.
gmx editconf -f protein_processed.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
3. Adding water molecule to the system.
gmx solvate -cp protein_newbox.gro -cs spc216.gro -o protein_solv.gro -p topol.top
4. Generating .tpr file; get ions.mdp here
gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr
5. Adding Ions to neutralised the system.
gmx genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1
6. Generating .tpr file; get minim.mdp here
gmx grompp -f minim.mdp -c protein_solv_ions.gro -p topol.top -o em.tpr
7. Running Energy Minimization to re-arrange ions.
gmx mdrun -v -deffnm em
8. Plotting Potential of the system.
gmx energy -f em.edr -o potential.xvg
9. Generating .tpr file; get nvt.mdp here
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
10. Running Temperature Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm nvt
11. Plotting Temperature of the system.
gmx energy -f nvt.edr -o temperature.xvg
12. Generating .tpr file; get npt.mdp here
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
13. Running Pressure Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm npt
14. Plotting Pressure of the system.
gmx energy -f npt.edr -o pressure.xvg
15. Plotting Density of the system.
gmx energy -f npt.edr -o density.xvg
16. Generating .tpr file; get md.mdp here
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
17. Running MD simulation.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm md_0_1
Please note -: It is just a tutorial for simplification of work flow detailed md tutorials can be found at http://www.mdtutorials.com/