1. Lab#9: GROMACS:
Lysozyme in Water
Asian University For Women
BINF 3016: Protein Modeling
(Lab - Fall 2022)
Syed Mohammad Lokman
Instructor
Asian University for Women

2. GROMACS
grompp
mdrun
energy
rms
gyrate
trjconv

3. gmx grompp -f xyz1.mdp -c xyz2.gro -r xyz2.gro -p xyz3.top -o xyz4.tpr-
-f = input file
.mdp = contains
settings for the
process
-c = coordinate file
.gro = contains
coordinate of
molecules
-r = restrain file
.gro = contains
coordinate of
molecules
-p = process file
.top = contains
topology of
molecules
-o = output file
.tpr = input file for
mdrun process in
gmx

4. gmx grompp -f xyz1.mdp -c xyz2.gro -r xyz2.gro -p xyz3.top -o xyz4.tpr-
-f = input file
.mdp = contains
settings for the
process
-c = coordinate file
.gro = contains
coordinate of
molecules
-r = restrain file
.gro = contains
coordinate of
molecules
-p = process file
.top = contains
topology of
molecules
-o = output file
.tpr = input file for
mdrun process in
gmx
gmx mdrun -v -deffnm xyz4
● em.log: ASCII-text log file of the EM process
● em.edr: Binary energy file
● em.trr: Binary full-precision trajectory
● em.gro: Energy-minimized structure
generate

6. Step 1: Installing GROMACS in Google Colab
1. Open a new google colab notebook, and rename the notebook as “lab#9_YourID”.
2. Connect to runtime
3. Enable GPU: From the top menu:
1. Runtime> Change Runtime Type> “GPU” under Hardware Accelerator option > Save (N.B.: If a prompt ask to
terminate other active runtime, do accordingly. Terminate the other runtime.)
4. Install GROMACS by using following code in the google colab:
# Download and unzip the compressed folder of GROMACS 2020.6 version
!wget https://raw.githubusercontent.com/pb3lab/ibm3202/master/software/gromacs.tar.gz
!tar xzf gromacs.tar.gz
# It is recommended to upgrade cmake
!pip install cmake --upgrade
!ln -sf /content/gromacs/bin/gmx /usr/bin/
!gmx --version
#Installing py3Dmol and biopython
!pip install py3Dmol biopython
#Importing py3Dmol for safety
import py3Dmol
#Make a new directory named "lab9"
%mkdir /content/lab9
#Change directory to "lab9"
%cd /content/lab9
#Check present working directory
!pwd

7. Step 2: Uploading Input files to Google Colab
1. Unzip the input files generated by Charmm-GUI.
2. Inside “charmm-gui” folder, find “gromacs” folder containing the necessary input files for MD production in GROMACS.
3. Upload these files inside lab9 folder. In your working google colab notebook, a folder named “lab9” is already created in the
previous step using “mkdir” command. (N.B.: to upload “toppar” folder, you have to create a folder named “toppar” first,
then upload the “toppar” folder files accordingly.)

8. ● Energy Minimization
● Equilibration
● MD Production
● Convert Trajectory
%%bash
gmx grompp -f step4 .0_minimization.mdp -c step3_input.gro -r step3_input.gro -p topol.top -n index.ndx -o em.tpr
gmx mdrun -v -deffnm em -nb gpu
%%bash
gmx grompp -f step4.1_equilibration.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr
gmx mdrun -v -deffnm nvt -nb gpu
%%bash
gmx grompp -f step5_production.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o md.tpr
gmx mdrun -v -deffnm md -nb gpu
#Using trjconv to extract only the protein atoms from the simulation trajectory
!echo "Protein" > options
!echo "Protein" >> options
!echo " "
!gmx trjconv -s md.tpr -f md.xtc -o md_protPBC.pdb -pbc mol -center < options
!gmx trjconv -s md.tpr -f md.xtc -o md_protPBC.xtc -pbc mol -center < options

9. ● Analysis: RMSD
● Analysis: Gyration
!gmx rms -s md.tpr -f md_protPBC.xtc -o rmsd.xvg -tu ns
#The radius of gyration of a protein is a measure of its compactness.
#If a protein is stably folded, it will likely maintain a relatively steady value of Rg.
#If a protein unfolds, its Rg will change over time. Let's analyze the radius of
gyration for lysozyme in our simulation:
!gmx gyrate -s md.tpr -f md_protPBC.xtc -o gyrate.xvg

10. ● Analysis: RMSD
● Analysis: Gyration
!gmx rms -s md.tpr -f md_protPBC.xtc -o rmsd.xvg -tu ns
#The radius of gyration of a protein is a measure of its compactness.
#If a protein is stably folded, it will likely maintain a relatively steady value of Rg.
#If a protein unfolds, its Rg will change over time. Let's analyze the radius of
gyration for lysozyme in our simulation:
!gmx gyrate -s md.tpr -f md_protPBC.xtc -o gyrate.xvg

11. Thank You