The Tutorials in this series are created using gromacs 2021.2 on Windows 10 OS Ubuntu Linux version 20.04 OS. Gromacs is an open source software to perform Molecular Dynamics (MD) simulation. It is popularly used in MD simulations of biological macromolecules and in polymer studies. 3D conformational space for macromolecules are generated for user analysis in the simulations. Structural coordinates for the individual atoms in a molecule, duration and sampling interval for MD, and force field details, are some of the inputs that are utilized, to calculate atomic interactions, associated energies, and conformational trajectories. Read more
Foss : Gromacs - English
Outline: About Gromacs official website Install Ubuntu 20.04 LTS app for Windows OS Install programs needed to build Gromacs Install make, gcc, build essential and cmake Download Gromac..
Outline: Register on VMD website for download VMD Install VMD 1.9.3 on Ubuntu Linux 20.04 OS Install VMD 1.9.3 on Windows 10 OS Open a PDB file in VMD Rotate molecule Change depth cue ..
Outline: About a PDB file PDB website Search and navigate the PDB website View biomolecule structure in the PDB website About FASTA file format Primary sequence of a protein Header de..
Outline: Flow chart for MD run for proteins in a solvent box from Gromacs manual Delete water molecules present in the input pdb file About pdb2gmx command and syntax About force field o..
Outline: About solvent molecule files that can be added to the system Solvate command View the solvated system in VMD About mdp file About grompp command Generate tpr binary file Use ..
Outline: About unfavorable interactions after the addition of solvent and ions View the solvated system in VMD Set up energy minimization mdrun command Verbose option to view the proces..
Outline: About temperature and pressure of the system Need for equilibration before the start of the MD simulation nvt.mdp and npt.mdp files Commands for NVT or temperature equilibration..
Outline: Load and play a trajectory file in VMD Settings to play and view trajectory About Timestep in Drawing method Display select specified frames Create new representation Notice ..
Outline: About input file for MD Timescale of motions Time taken for MD Run MD for 1ns About Output files About Data Analysis, PCA, energetics About xtc trajectory file View trajecto..