Connect with us

MD Simulation

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

Dr. Muniba Faiza

Published

on

How to solve ‘Could NOT find CUDA: Found unsuitable version “10.1”‘ error during GROMACS installation?

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.

The error we experience most while compiling GROMACS with CUDA is ‘Could NOT find CUDA: Found unsuitable version “10.1”‘. It occurs when you still haven’t wholly uninstalled CUDA’s old version (here, 10.1).

Before proceeding further, if you are installing GROMACS with CUDA, ensure to remove the previous CUDA toolkit and NVIDIA drivers. For details, read this article.

Now let’s get back to solving the error, you will have to remove the symlink of the previous CUDA version and then link the new one as shown below.

Removing old CUDA symlink

  • Go to /usr/local/ (or where your CUDA is installed, generally, it is /usr/local/).
  • Open a terminal and change to /usr/local
    $ cd /usr/local
  • Remove the ‘cuda’ directory as follows:
    $ sudo rm cuda

Create a symlink to the new CUDA version

  • Paste the following command in the terminal:
    $ sudo ln -s /usr/local/cuda-11.7 /usr/local/cuda

This should solve the error. But if you still get the same error then add the CUDA root dir (-D CUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda) path in your cmake command as shown below:

$ sudo cmake .. -DGMX_BUILD_OWN_FFTW=OFF -DREGRESSIONTEST_DOWNLOAD=OFF -DMAKE_C_COMPILER=gcc -DGMX_GPU=CUDA -D CUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_MPI=OFF -DREGRESSIONTEST_PATH=/your/pwd/path/here/Downloads/regressiontests-2021

 


References

  1. 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. SoftwareX1, 19-25.

Further Reading

Tutorial: Molecular dynamics (MD) simulation using Gromacs

Method-2: Installing GROMACS on Ubuntu 20.04 with CUDA GPU Support

How to take snapshots of structure at specific times in GROMACS?

Installing GROMOS96 on Ubuntu

 

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

MD Simulation

Energy minimization and equilibration of simple protein using NAMD & VMD.

Dr. Muniba Faiza

Published

on

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.

(more…)

Continue Reading

MD Simulation

Generating topology of molecule for AMBER forcefield for GROMACS.

Dr. Muniba Faiza

Published

on

Generating topology of molecule for AMBER forcefield for GROMACS.

In this article, we will generate the topology of a small molecule for AMBER forcefield to be used in MD simulation using GROMACS.

(more…)

Continue Reading

MD Simulation

How to visualize output plots of MD simulation (GROMACS)?

Dr. Muniba Faiza

Published

on

How to visualize output plots of MD simulation (GROMACS)?

Visualizing plots of molecular dynamics simulation is easy once you have generated them. Previously, we provided a few articles on MD output analysis (check the Further Reading section). This article explains how you can easily visualize the plots generated from GROMACS output. (more…)

Continue Reading

MD Simulation

How to calculate number of steps (nsteps) for MD simulation run?

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

MD Simulation

How to install GROMACS on Apple M1 (MacOS)?

Dr. Muniba Faiza

Published

on

Installing 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…)

Continue Reading

MD Simulation

How to take snapshots of structure at specific times in GROMACS?

Published

on

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…)

Continue Reading

MD Simulation

GROMACS: Uses & Applications

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

MD Simulation

Easy installation of GROMACS on Ubuntu 18.04 & 20.04

Dr. Muniba Faiza

Published

on

Installing GROMACS on ubuntu

We have provided several articles on GROMACS [1] installation on Ubuntu including the easy installation method for GROMACS version 5.x.x. In this article, we will provide shell scripts to install the latest (2021 series) of GROMACS on Ubuntu 18.04 and 20.04. (more…)

Continue Reading

MD Simulation

How to create an index file in GROMACS for MD simulation?

Dr. Muniba Faiza

Published

on

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. (more…)

Continue Reading

MD Simulation

How to generate topology of small molecules & ligands for MD Simulation?

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

MD Simulation

Tutorial: MD Simulation of small organic molecules using GROMACS

Dr. Muniba Faiza

Published

on

MD Simulation of small molecules

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…)

Continue Reading

MD Simulation

Tutorial: MD simulation with mixed solvents using GROMACS

Dr. Muniba Faiza

Published

on

MD simulation with mixed solvents

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…)

Continue Reading

MD Simulation

Tutorial: MD simulation output analysis of a complex using GROMACS

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

MD Simulation

How to submit MD simulation job on a cluster server using PBS script?

Dr. Muniba Faiza

Published

on

MD Simulation on cluster server

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…)

Continue Reading

MD Simulation

Method-1: Installing GROMACS on Ubuntu with CUDA GPU Support

Dr. Muniba Faiza

Published

on

Install gromacs with gpu acceleration

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…)

Continue Reading

MD Simulation

Installing GROMOS96 on Ubuntu

Dr. Muniba Faiza

Published

on

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…)

Continue Reading

MD Simulation

MD Simulation using GROMACS: Things to remember

Dr. Muniba Faiza

Published

on

MD Simulation

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…)

Continue Reading

MD Simulation

Video Tutorial: MD Simulation using GROMACS

Dr. Muniba Faiza

Published

on

Video Tutorial: MD simulation using GROMACS

This is a video tutorial of our existing article “Molecular Dynamics (MD) Simulation using GROMACS“.

Continue Reading

MD Simulation

Tutorial: MD Simulation of a Protein-Ligand Complex using GROMACS

Dr. Muniba Faiza

Published

on

md simulation of protein-ligand complex

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…)

Continue Reading

MD Simulation

Installing CHARMM on Ubuntu

Published

on

CHARMM installation on Ubuntu

CHARMM (Chemistry at Harvard Molecular Mechanics) is a molecular simulation program that can be used for simulation of macromolecules, complexes, and many-particle systems [1]. In this article, we will install the nonprofit/academic version of CHARMM on Ubuntu. (more…)

Continue Reading

LATEST ISSUE

ADVERT