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Gromacs Quick Start

GROMACS Quick Start


Official Documentation:

https://manual.gromacs.org/current/user-guide/index.html


Gromacs Server and Environment:


Gromacs is pre-installed on a Levich server and user accounts are initilized to include Gromacs path.

In case you want to see how the Gromacs environment was set, Here it is:
In file ~/.profile, the last line points to gromacs environment initialization:
source /usr/local/gromacs/bin/GMXRC


Users are expected to install their own Python and Python modules.

Install Conda Python and Python modules:
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh   (answer yes to initialize Minicoda3)

Logout and back in to have conda environment, then run:

conda install numpy scipy matplotlib pandas

Conda can be deactivated or reactivated by command:
conda deactivate
conda activate


Gromacs Command

Main Command: gmk

Examples: 

gmx -h                                          (print help)
gmk -v                                           (show version)
gmx help [module]                   (documentation of a module)


Example 1: Lysozyme

In this example, we are going to use hen egg white lysozyme (PDB ID 1AKI) to run a MD simulation.


Prepare structure and topology files

Create a working directory:
mkdir lysozyme
cd lysozyme

Download a pdb file from Protein Data Bank
getpdb 1aki

Pymol molecule structure viewer is preinstalled on the system. Due the Python dependency, one needs to deactivate conda to run Pymol.
conda deactivate
pymol 1aki.pdb

After verifying structure, quit pymol and activate conda again.
conda activate

Delete crystal water molecules. Water in the pdb file are crystal water molecules. Gromacs has its own way to add solvent water.
grep -v HOH 1aki.pdb > 1aki_clean.pdb

Create topology file and process the structure file
gmx pdb2gmx -f 1aki_clean.pdb -o 1AKI_processed.gro -water spce

When it will prompts to select a force field, select choice 15 - OPLS force field.

The explanation of pdb2gmx module can be found by running:
gmx help pdb2gmx

-f 1aki_clean.pdb:    Input file
-o 1AKI_processed.gro:   Output file for Gromacs use
-water spce:   The model to build solvent water

Other two files are 
  • topol.top   Topology file defines atom and bond parameters.
  • posre.itp   Position restraint file

Define the simulation box and solvent

 

Step 1: Define the box dimensions using the editconf module

gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic

This command use module editconf to center and define a box.

  • -f 1AKI_processed.gro:  Input file
  • -o 1AKI_newbox.gro: Output file, the box is 0,0,0 and the coordinates at the bottom line
  • -c:   center the box
  • -d 1.0:  Leave at least 1 nm at the edge
  • -bt cubic: Use cubic box.  There are other choices such as rhombic dodecahedron.

 

Step 2: Fill the box with water using the solvate module

gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top

This command uses module solvate to add water molecules into the box.
  • -cp 1AKI_newbox.pro: Configuration of the protein from the named file
  • -cs spc216.gro: Configuration of the solvent. Spc216.gro is a generic equilibrated 3-point solvent model good for SPC, SPC/E, or TIP3P water.
  • -o 1AKI_solv.gro: Output file name
  • -p topol.top: Topology file name. Solvate module will update this file to include both protein molecule and solvate (SOL) line

 

Add ions

In topology file [ atom ]  section, the protein total charge is calculated. The charge at the end of this section is the net charge.

1960   opls_272    129    LEU     O2    682       -0.8    15.9994   ; qtot 8

In this example, the net charge is 8.

In MD simulation, we need to balance the charge with ions so that we have a neutral system.

 

 

Example 2:

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