MD Simulation
How to create an index file in GROMACS for MD simulation?
MD simulation is a tricky technique if you don’t understand what you are doing through various parameters and algorithms in GROMACS [1]. That may lead to several errors. In this article, we are going to create an index file for the protein groups in GROMACS to solve such errors.
While you have to restrain some groups or atoms or residues during simulation, you need an index file. GROMACS has default groups but it may be possible that the group you are working with is not separately mentioned in the index file. Therefore, you have to create one specifying the group protein or residues or atoms to restrain. In such a case, without using this file you may encounter some errors. For example,
“Fatal error:
Group Protein referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the ‘-n’ option
of grompp.”
Here, you must create an index file and pass it to the grompp command for the MD run.
Creating an index file
To create an index file, we will use the make_ndx module of GROMACS. Open the terminal (Ctrl+Alt+T) and type the following command:
$ gmx make_ndx –f protein.pdb –o protein.ndx
It will display the default groups. If you can find your group in the displayed list then select it (there are barely minimum chances of that).
Now, to create a new group of atoms (let’s say), type the following command.
$ a PO4
It will add this new group to the list of all default groups.
If you want to add a few residues, then type this:
$ r 45 56 58 78 106 180
For example, previously it was showing 11 default groups, not it will show 12 as shown below.
12 r 45 56 58 78 106 180: 53 atoms
It shows you a default name for this group (i.e., r_45_56_58_78_106_180). You can rename it as ‘residues‘ using the following command:
$ name 12 rest_residues
Now, it will show you all 12 groups on the list. Finally, quit by typing q
Using the index file
Now pass this index file to the grompp command as shown below:
$ gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n protein.ndx -o md_0_1.tpr
This is not necessary that you create this file before this command only. You can create this before nvt or npt simulation also.
If error persists
To this point, your error should be gone. But in some cases, it may reappear, then you have to freeze these residues by adding a few lines in the md.mdp file.
Open the md.mdp file and add the following lines:
energygrps_excl = rest_residues rest_residues rest_residues SOL ! To remove computation of nonbonding interactions between the frozen groups with each other and surroundings (i.e. the solvent, SOL)
freezegrps = rest_residues ! Index group to freeze
freezedim = Y Y Y ! Freeze this group in all directions, x, y, and z
Now use the grompp command as explained above.
References
- Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1, 19-25.
Further Reading
How to generate topology of small molecules & ligands for MD Simulation?
Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS
Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support
Tutorial: MD Simulation of small organic molecules using GROMACS
MD Simulation
Energy minimization and equilibration of simple protein using NAMD & VMD.
In this tutorial, we will perform energy minimization and equilibration of a simple protein using NAMD [1] & VMD [2]. We are using insulin (PDB ID: 2wfu) for this tutorial.
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MD Simulation
How to visualize output plots of MD simulation (GROMACS)?
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MD Simulation
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Compiling GROMACS [1] with GPU can be trivial. Previously, we have provided a few articles on the same. In this article, we will solve an error frequently occurring during GROMACS installation.
MD Simulation
How to calculate number of steps (nsteps) for MD simulation run?
While doing molecular dynamics (MD) simulation, it can be difficult to calculate the number of steps or nsteps for an MD run accurately. In this article, we will learn to calculate nsteps for an MD run. (more…)
MD Simulation
How to install GROMACS on Apple M1 (MacOS)?
We have provided a few articles on GROMACS installation on Ubuntu. In this article, we are going to install GROMACS [1] on Mac OS. (more…)
MD Simulation
How to take snapshots of structure at specific times in GROMACS?
It is important to see the behavior of protein during an MD simulation. This can be achieved by taking snapshots in the form of PDB format. In this article, we have provided a few commands that you can use to take snapshots of a complete system or protein during MD simulation. (more…)
MD Simulation
GROMACS: Uses & Applications
GROMACS stands for GROningen MAchine for Chemical Simulations [1]. It is a very popular and one of the most widely used open-source bioinformatics software. It is generally used for molecular dynamics simulation of macromolecules. In this article, we will explain its uses and applications in bioinformatics studies. (more…)
MD Simulation
Easy installation of GROMACS on Ubuntu 18.04 & 20.04
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MD Simulation
How to generate topology of small molecules & ligands for MD Simulation?
Generating the topology of small molecules/ligands is an important step in molecular dynamics (MD) Simulation. We explained it in previous articles as part of MD simulation tutorials. In this article, we will explain how can you generate the topology of ligands for MD simulation of complex or small molecules only. (more…)
MD Simulation
Tutorial: MD Simulation of small organic molecules using GROMACS
GROMACS [1] offers a vast range of functions when it comes to molecular dynamics simulation. Today, we are going to explore it for the simulation of small organic molecules. (more…)
MD Simulation
Tutorial: MD simulation with mixed solvents using GROMACS
In this tutorial, we are performing MD simulation in mixed solvents of methanol and water using GROMACS [1,2]. You can follow our previous articles for MD simulation of a simple protein and a protein-ligand complex. (more…)
MD Simulation
Tutorial: MD simulation output analysis of a complex using GROMACS
We have provided several tutorials on molecular dynamics (MD) simulation (please check further reading section). They include installation of simulation software, simulation of a simple protein, and a complex. In this article, we will analyze the GROMACS [1] output of MD simulation of a complex. (more…)
MD Simulation
How to submit MD simulation job on a cluster server using PBS script?
Molecular dynamics (MD) simulation is one of the most widely used methods in bioinformatics. It needs high computation time and therefore, performed on workstations and servers. It requires software to upload and download files to and from the server. In this article, we have explained how to submit MD simulation jobs on cluster computers using PBS scripts. (more…)
MD Simulation
Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support
GROMACS [1] is one of the most popular software in bioinformatics for molecular dynamic (MD) studies of macromolecules. We have provided different tutorials regarding MD simulation using GROMACS including its installation on Ubuntu. In this article, we will install GROMACS with GPU acceleration. (more…)
MD Simulation
Installing GROMOS96 on Ubuntu
GROMOS96 is a well-known software package used for biomolecular simulations [1]. It can be used for the molecular dynamics simulation of protein, peptide, and protein-ligand complex as well. In this article, we will install GROMOS96 on Ubuntu. (more…)
MD Simulation
MD Simulation using GROMACS: Things to remember
Molecular dynamics (MD) simulation is considered amongst the important methods in bioinformatics. Installation of MD simulation software and execution of their commands is critical. It requires several parameters to be considered before performing simulations. A single mistake may result in impractical outputs. In this article, we will discuss such important things to remember during the MD simulation and installation and execution of its software (GROMACS) [1,2]. (more…)
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Video Tutorial: MD Simulation using GROMACS
This is a video tutorial of our existing article “Molecular Dynamics (MD) Simulation using GROMACS“.
MD Simulation
Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS
Previously, we have provided a tutorial on molecular dynamics (MD) simulation of a protein using GROMACS [1] and its result analysis [2]. In this article, we will perform MD simulation for a protein-ligand complex using GROMACS [3, 4]. (more…)
MD Simulation
Installing CHARMM on Ubuntu
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