How to do MDs

Prepare the system

Justin's tutorials are always the good starting points (here), especially the "Lysozyme in water" one (here).

Simple steps to prepare a system, and it usually works! (script can be found here)

# Create a cubic box of 2 nm on each side and place the system to the center and align its principle axes to the reference axes
# -princ usually helps to reduce your system size
gmx editconf -f conf.gro -o editconf.gro -bt cubic -d 2 -c -princ
# Solvate the box
gmx solvate -cp editconf.gro -o solvate.gro -p topol.top
# Add ions to make it neutral and of 0.15 M NaCl
# If you want KCl, add -pname K
gmx grompp -f ions.mdp -c solvate.gro -o ions.tpr -p topol.top
gmx genion -s ions.tpr -o ionized.gro -conc 0.15 -neutral -p topol.top

Things to note:

1. You can find ions.mdp here.
2. Biological systems might require surprisingly large boxes, if you are interested, read this.

Standard MD

A standard MD includes steps as follows:

1. Energy minimization
2. Annealing
3. Pre-equilibrium
4. Production run

Here are some standard run scripts.

Things to note:

1. In step2-3, position restraints have been added to favor the initial structures (usually crystal)
2. You may consider release the restraints step-wisely