Lysozyme tutorial

This tutorial follows Justin Lemkul’s lysozyme tutorial. We will not explain each individual step as this can be found on Justin’s webpage, but we will link to each page and show the AiiDA equivalant command.

Please also note the slight differences in commands between the tutorial and that by Justin Lemkul is simply down to the way we are recording provenance requires non-interactive input into the gromacs tools.

Also at each of the below steps you should run verdi to view the status of the submitted process before moving onto the next step, you do this by:

verdi process list -a

A successfully finished process will exit with code [0].

1. We will start from the pbd2gmx step of Justin’s tutorial:

   gmx_pdb2gmx -f 1AKI_clean.pdb -ff oplsaa -water spce -o 1AKI_forcefield.gro -p 1AKI_topology.top -i 1AKI_restraints.itp
   

2. Next we will create the box and solvate

   Firstly the box:

   gmx_editconf -f 1AKI_forcefield.gro -center 0 -d 1.0 -bt cubic -o 1AKI_newbox.gro
   

   Then solvate:

   gmx_solvate -cp 1AKI_newbox.gro -cs spc216.gro -p 1AKI_topology.top -o 1AKI_solvated.gro
   

3. Add ions

   Firstly we will use the grompp preprocessor:

   gmx_grompp -f ions.mdp -c 1AKI_solvated.gro -p 1AKI_topology.top -o 1AKI_ions.tpr
   

   Followed by genion:

   gmx_genion -s 1AKI_ions.tpr -p 1AKI_topology.top -pname NA -nname CL -neutral true -o 1AKI_solvated_ions.gro
   

4. Then minimise the structure

   Firstly we will use grompp:

   gmx_grompp -f min.mdp -c 1AKI_solvated_ions.gro -p 1AKI_topology.top -o 1AKI_minimised.tpr
   

   Then mdrun to minimise:

   gmx_mdrun -s 1AKI_minimised.tpr -c 1AKI_minimised.gro -e 1AKI_minimised.edr -g 1AKI_minimised.log -o 1AKI_minimised.trr
   

5. Now we will equilibrate with NVT

   Firstly we will use grompp:

   gmx_grompp -f nvt.mdp -c 1AKI_minimised.gro -r 1AKI_minimised.gro -p 1AKI_topology.top -o 1AKI_nvt.tpr
   

   Then mdrun to equilibrate NVT:

   gmx_mdrun -s 1AKI_nvt.tpr -c 1AKI_nvt.gro -e 1AKI_nvt.edr -g 1AKI_nvt.log -cpo 1AKI_nvt.cpt -o 1AKI_nvt.trr
   

6. Followed by equilibration with NPT

   Firstly we will use grompp:

   gmx_grompp -f npt.mdp -c 1AKI_nvt.gro -r 1AKI_nvt.gro -t 1AKI_nvt.cpt -p 1AKI_topology.top -o 1AKI_npt.tpr
   

   Then mdrun to equilibrate NPT:

   gmx_mdrun -s 1AKI_npt.tpr -c 1AKI_npt.gro -e 1AKI_npt.edr -g 1AKI_npt.log -cpo 1AKI_npt.cpt -o 1AKI_npt.trr
   

7. We are now ready for production MD.

   Firstly we will use grompp:

   gmx_grompp -f md.mdp -c 1AKI_npt.gro -t 1AKI_npt.cpt -p 1AKI_topology.top -o 1AKI_prod.tpr
   

   Then mdrun for production run:

   gmx_mdrun -s 1AKI_prod.tpr -c 1AKI_production.gro -e 1AKI_production.edr -g 1AKI_production.log -o 1AKI_production.trr
   

   If running on GPU then something like:

   gmx_mdrun -s 1AKI_prod.tpr -c 1AKI_production.gro -e 1AKI_production.edr -g 1AKI_production.log -o 1AKI_production.trr -bonded gpu -nb gpu -pme gpu -ntmpi 1 -ntomp 5 -pin on
   

That is it!