Using energy groups in Gromacs

Goals of this tutorial

At the end of this tutorial, you should be able to:

• Visualize the system using visual molecular dynamics (VMD) studio

• Generate energy groups from molecular dynamics parameter (mdp) files

• Using the energy groups, compute Lennard-Jones energies using "gmx -rerun" command

Software required for this tutorial

• Bash terminal: Main language used to run code

  • On Mac: Command + space, type in "Terminal" and hit enter

  • On Windows 10:

    • Install gitbash: https://gitforwindows.org/

    • Alternatively, use the ubuntu add-on: https://www.omgubuntu.co.uk/2016/08/enable-bash-windows-10-anniversary-update

• Gromacs: Simulation package [Link for installation] (Version 2016)

• Visual molecular dynamics studio (VMD, optional) [Link]: Used to visualize simulations

Files for this tutorial

All input/output files are downloadable through GitLab [Link]. To download, click the "Download" button and select "Download this directory".

• P_in_S-PET_trimer-acetone-300_K: Simulation folder containing trajectories.

  • "poly_solv_prod*" prefix contains 10 ns production trajectories in the NPT ensemble

  • poly_solv.top: topology file for the system

  • prod.mdp: mdp file for production run

• images: Contains images used for this tutorial

Step 1: Defining energy groups using gmx make_ndx

Run the following command in terminal to generate an index file containing PET trimer:

gmx make_ndx -f poly_solv_prod.tpr -o energy_group_index.ndx << INPUTS

keep 0

r PT3

r ACE

q

INPUTS

The command will create an index file with PET trimer (i.e. PT3) and acetone (ACE) as separate groups.

Step 2: Edit MDP file to include energy groups

The following function edits the production mdp file (prod.mdp) and adds specific energy groups; copy and paste this into terminal or include this as part of your ~/.bashrc

function mdp_add_energy_groups ()

{

input_mdp_file_="$1";

output_mdp_file_="$2";

energy_groups_="$3";

cp -r "${input_mdp_file_}" "${output_mdp_file_}";

echo "" >> "${output_mdp_file_}";

echo "; ENERGY GROUPS " >> "${output_mdp_file_}";

echo "energygrps = ${energy_groups_}" >> "${output_mdp_file_}";

echo "----- mdp_add_energy_groups -----";

echo "--> Created ${output_mdp_file_} from ${input_mdp_file_}";

echo "--> Added energy groups: ${energy_groups_}"

}

Then, add PET and ACE as an energy group by running:

mdp_add_energy_groups "prod.mdp" "prod_energy_groups.mdp" "PT3 ACE"

This function copies prod.mdp into a new file called prod_energy_groups.mdp and adds energy groups to the bottom:

; ENERGY GROUPS

energygrps = PT3 ACE

Step 3: Create a new *.tpr file with the new *.mdp file and rerun Gromacs

Gromacs needs a new *.tpr file with the energy groups, so create it using grompp:

gmx grompp -f "prod_energy_groups.mdp" -c "poly_solv_prod.gro" -p "poly_solv.top" -o "poly_solv_prod_energy_groups.tpr" -n "energy_group_index.ndx" -maxwarn 5

This should create a new file called "poly_solv_prod_energy_groups.tpr". Then, perform mdrun again using the "-rerun" flag:

gmx mdrun -v -nt 1 -s poly_solv_prod_energy_groups.tpr -rerun poly_solv_prod.xtc -e poly_solv_prod_energy_groups.edr

This should only take a couple of seconds to run, which will go through the trajectory and compute energies defined as "energygrps."