Equilibration

Equilibration

Before benchmarking or running a production run, your MD simulation system must be relaxed through equilibration.

We use CHARMM-GUI to prepare MD simulation systems.

SFTP charmm-gui.tgz to Bridges.

SSH to Bridges.

tar -xvf charmm-gui.tgz

cd charm-gui-(number)

Edit the README, step6.1_equilibration.mdp and step6.2_equilibration.mdp (see attached files below).

Module load gromacs or source gromacs

csh README

Once the equilibration simulations are run, you will find topology (tpr)and trajectories (trr) files. You can place the protein at the center of the MD system by using trjconv. For example:

gmx trjconv -f step6.6_equilibration.trr -s step6.6_equilibration.tpr -o step6.6_equilibration.xtc -pbc mol -center -ur compact