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GROMACS Tutorial. This example will guide a new user through the process of setting up a simulation system containing a protein (lysozyme) in a box of water, with ions. Each step will contain an explanation of input and output, using typical settings for general use.
Lysozyme Tutorial. We must download the protein structure file with which we will be working. For this tutorial, we will utilize hen egg white lysozyme (PDB code 1AKI). Go to the RCSB website and download the PDB text for the crystal structure.
For this tutorial, a few basic tools will be introduced. The first is trjconv, which is used as a post-processing tool to strip out coordinates, correct for periodicity, or manually alter the trajectory (time units, frame frequency, etc).
If a protein is stably folded, it will likely maintain a relatively steady value of Rg. If a protein unfolds, its Rg will change over time. Let's analyze the radius of gyration for lysozyme in our simulation: Choose group 1 (Protein) for analysis.
Equilibration of pressure is conducted under an NPT ensemble, wherein the Number of particles, Pressure, and Temperature are all constant. The ensemble is also called the "isothermal-isobaric" ensemble, and most closely resembles experimental conditions.
The solvated, electroneutral system is now assembled. Before we can begin dynamics, we must ensure that the system has no steric clashes or inappropriate geometry. The structure is relaxed through a process called energy minimization (EM). The process for EM is much like the addition of ions.
As of version 4.6, GROMACS supports the use of GPU accelerators for running MD simulations. With the release of version 2018, the nonbonded interactions and PME are calculated on the GPU, with only bonded forces calculated on the CPU cores.
To begin real dynamics, we must equilibrate the solvent and ions around the protein. If we were to attempt unrestrained dynamics at this point, the system may collapse. The reason is that the solvent is mostly optimized within itself, and not necessarily with the solute.
Lysozyme in Water: The intent of this tutorial is to give new users a basic introduction into the tools used to prepare, run, and perform simple analysis on a "typical" system with GROMACS.
The tool for adding ions within GROMACS is called genion. What genion does is read through the topology and replace water molecules with the ions that the user specifies.