GROMACS_TUTORIAL

What is molecular dynamics simulation??

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.

Gromacs commands for simulating protein-protein complex in solvent

Requirements:

*Install Xmgrace for generating graphs from .xvg files

> Create a file containing all the essential parameter files including the processed .pdb file

> Open terminal direct to the PWD which contains all the essential parameter files

Step 1: Generating protein topology files

"gmx pdb2gmx -f complex.pdb -o complex_processed.gro -water spce"

Type 15 at the command prompt, followed by 'Enter

Additional options: in case of missing atoms use -missing, in case of other error use -ignh to ignore

Step 2: Define unit cubical cell/box of 1 Amstrong

"gmx editconf -f complex_processed.gro -o complex_newbox.gro -c -d 1.0 -bt cubic"

Step 3: Adding solvent (water)

"gmx solvate -cp complex_newbox.gro -cs spc216.gro -o complex_solv.gro -p topol.top"

Step 4: Adding ions

"gmx grompp -f ions.mdp -c complex_solv.gro -p topol.top -o ions.tpr"

Step 5: Setting the net charge zero

"gmx genion -s ions.tpr -o complex_solv_ions.gro -p topol.top -pname NA -nname CL -neutral"

Step 6: Energy minimization

"gmx grompp -f minim.mdp -c complex_solv_ions.gro -p topol.top -o em.tpr"

"gmx mdrun -v -deffnm em"

Step 7: Generate potential energy graph#

"gmx energy -f em.edr -o potential.xvg"

> At the prompt, type "10 0" to select Potential (10); zero (0) terminates input.

"xmgrace potential.xvg"

Step 8: NVT equilibration

"gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr"

"gmx mdrun -deffnm nvt"

"gmx energy -f nvt.edr -o temperature.xvg"

> At the prompt, type "16 0"

> xmgrace temperature.xvg

Step 9: NPT equilibration

"gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr"

"gmx mdrun -deffnm npt"

"gmx energy -f npt.edr -o pressure.xvg"

> At the prompt, type "18 0"

"gmx energy -f npt.edr -o density.xvg"

> At the prompt, type "24 0"

Step 10: Production MDrun

"gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr"

Step 10: Execution of MD

> either:

"gmx mdrun -deffnm md_0_1"

> or

"gmx mdrun -deffnm md_0_1 -nb gpu"