MD simulations of calmodulin

Set up gmx if not in the path:

GMX=/usr/local/gromacs/bin/gmx

Get the CHARMM36 forcefield:

wget http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/charmm36-jul2022.ff.tgz -O charmm36-jul2022.ff.tgz
tar -xvf charmm36-jul2022.ff.tgz
rm charmm36-jul2022.ff.tgz

Get the PDB file from https://www.rcsb.org/structure/1cfd :

wget https://files.rcsb.org/download/1CFD.pdb

Pre-process the file, select forcefield:

$GMX pdb2gmx -f 1CFD.pdb -o processed.gro -ignh

Chose CHARMM from local folder (usually option 1), select TIP3P for water.

Define the solvation box:

$GMX editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt cubic

Solvate:

$GMX solvate -cp newbox.gro -o solv.gro -p topol.top

Add ions:

touch ions.mdp
$GMX grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
$GMX genion -s ions.tpr -o solv_CAL.gro -p topol.top -np 4 -pname CAL -pq 2 -nn 0
$GMX grompp -f ions.mdp -c solv_CAL.gro -p topol.top -o ions.tpr
$GMX genion -s ions.tpr -o solv_ions.gro -conc 0.15 -p topol.top -pname NA -nname CL -neutral

Select group SOL

Get the mdp files for energy minimization , nvt and npt equilibration and production md.

Run energy minimization:

$GMX grompp -f emin-charmm.mdp -c solv_ions.gro -o em.tpr
$GMX mdrun -v -deffnm em

Get the energy plot (to get plain .dat file, use -xvg none option):

$GMX energy -f em.edr -o potential.xvg

Select the potential energy.

Run temperature equilibration:

$GMX grompp -f nvt-charmm.mdp -c em.gro -r em.gro -o nvt.tpr
$GMX mdrun -v -deffnm nvt

Check the temperature:

$GMX energy -f nvt.edr -o temperature.xvg

Select the temperature.

Equilibrate pressure:

$GMX grompp -f npt-charmm.mdp -c nvt.gro -r nvt.gro -o npt.tpr
$GMX mdrun -v -deffnm npt

Check the pressure:

$GMX energy -f npt.edr -o pressure.xvg

Select the pressure.

Production run:

$GMX grompp -f md-charmm.mdp -c npt.gro -t npt.cpt -o md.tpr
$GMX mdrun -v -deffnm md

To remove jumps of atoms through the periodic boundary, use the following command:

$GMX trjconv -s md.tpr -f md.xtc -o md_center.xtc -center -pbc mol

Select protein as a molecule to center the trajectory around and save the entire system again.