I was reading about Accelerated Molecular Dynamics (aMD) ( Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules | The Journal of Chemical Physics | AIP Publishing, or a recent application here Frontiers | Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water). In summary, protein torsional energy terms and total potential energies of the system are modified with a simple scheme so as to lower energy barriers and thus accelerate conformational sampling, without any prior knowledge of collective variables (other than that torsions are important in proteins). There is an Amber tutorial on this, but I was wondering if this could be done easily in Gromacs, or if anyone knows of any plugins / patches that do this.
ummhh 🤔 Enabling CUDA could speed up your MD simulation 10X, and I personally did a 1-microsecond simulation of a protein-ligand complex in less than 4 days.
yet without compromising the integrity of the results.
For Gromacs, the process is straightforward:
----INSTALL UBUNTU-----
UPGRADE AND UPDATE LIBRARIES OF UBUNTU BY FOLLOWING COMMANDS
Commands:
sudo apt update
sudo apt upgrade
sudo apt install gcc
sudo apt install cmake
sudo apt install libfftw3-dev
OR
sudo apt-get install -y libfftw3-dev
sudo apt-get install build-essential
--------------- GROMACS MANUAL COMPILATION --------------
Download Gromacs from: Downloads - GROMACS 2024.2 documentation
Download CUDA Toolkit: CUDA Toolkit 12.5 Update 1 Downloads | NVIDIA Developer
Follow the steps and copy the commands
tar xfz gromacs-2020.2.tar.gz
cd gromacs-2024.2
mkdir build
cd build
cmake … -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
make
make check
sudo make install
source /usr/local/gromacs/bin/GMXRC
continue your MD simulation Happily 😍
As far as I know, GROMACS does not have support for aMD.