This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to perform COM Pulling using GROMACS Wizard. Reference: We will use the same system, 2BEG, as in the Umbrella Sampling tutorial by Justin A. Lemkul. 1. Loading the system First, load the system: go to Home menu > Fetch and load 2BEG from the RCSB PDB in mmCIF or PDB format. When loading the structure into SAMSON a pop-up might appear with import options depending on the…
This section is a part of the GROMACS Wizard tutorial. This tutorial demonstrates how to perform Umbrella Sampling using GROMACS Wizard. To perform Umbrella Sampling you first need to obtain a set of initial conformations. You can do it in one of the following ways: From GROMACS trajectory obtained from some simulation, e.g. by performing COM pulling simulation. From a set of conformations or a path (trajectory) created outside SAMSON or in SAMSON. Then you need to perform NPT equilibration and…
This section is part of the GROMACS Wizard tutorial. GROMACS automatically generates standard index groups for your system based on its structure (e.g., protein, water, ions, etc.). But sometimes you might want to add custom index groups that we later be useful for analysis or during the simulation (e.g., as pull coordinate groups). You can do this thanks to GROMACS Wizard which allows you to use the extensive selection mechanisms available in SAMSON (see User Guide: Selecting). When dealing with…
“GROMACS uses periodic boundary conditions, combined with the minimum image convention: only one – the nearest – image of each particle is considered for short-range non-bonded interaction terms. For long-range electrostatic interactions this is not always accurate enough, and GROMACS therefore also incorporates lattice sum methods such as Ewald Sum, PME and PPPM.” (GROMACS Manual: Periodic boundary conditions) GROMACS Wizard supports the following shapes for space-filling unit cells: Cubic, Orthorhombic, Triclinic, Rhombic dodecahedron, Truncated octahedron. You can choose which unit…
This section is part of the GROMACS Wizard tutorial. GROMACS Wizard allows you to launch GROMACS computations for NVT Equilibration, NPT Equilibration, Production Molecular Dynamics Simulation steps in the Cloud in just a few clicks. In this section, you will learn how to launch GROMACS computations in the Cloud from GROMACS Wizard on an example of the NVT Equilibration step. This procedure is the same for NPT Equilibration and Production Molecular Dynamics Simulation steps. Prerequisites Before going further, please first read…
This section is a part of the GROMACS Wizard tutorial. For each of the Energy Minimization, NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics Simulation steps you can provide custom molecular dynamics parameters (MDP) using the graphical user interface or by loading them from an existing GROMACS molecular dynamics parameter file (an .mdp file). These parameters are populated with their default values. You can see some of the parameters directly in the tabs and the other parameters can be accessed…
This section is a part of the GROMACS Wizard tutorial. Using a custom GROMACS version GROMACS Wizard comes with one of the latest versions of GROMACS. But it also provides you with the possibility to use your own version of GROMACS for local computations. This might be useful if you would like to use the GROMACS package installed on your system or use a specific GROMACS version for reproducibility reasons. To use a locally installed version of GROMACS, press the Settings…
This section is part of the GROMACS Wizard tutorial. Once the equilibration of the system is completed – the system’s temperature and density have stabilized at the desired values – we can finally run a production molecular dynamics (MD) simulation. Switch to the Simulate tab. Selecting input structure When launching the NPT Equilibration step, GROMACS Wizard requires you to provide one of the following: The path to a GRO file resulting from the previous step: either a GRO file resulting from…
This section is part of the GROMACS Wizard tutorial. Once the system has been successfully minimized and the system’s temperature has stabilized at the desired value, it is necessary to apply pressure to the system until it reaches the correct density. This second equilibration phase is aimed at stabilizing the system’s density at the desired value by performing equilibration using the NPT ensemble (constant Number of particles, Pressure, and Temperature) also known as “isothermal-isobaric”. Switch to the Equilibrate (NPT) tab. Selecting input…
This section is part of the GROMACS Wizard tutorial. Once the system has been successfully minimized, it is necessary to Equilibrate the system to bring it to the desired temperature and pressure/density and stabilize it. Equilibration is often conducted in two phases. The first one is aimed at bringing the system to the desired temperature (the one that you would like to simulate) and stabilizing it by performing equilibration using the NVT ensemble (constant Number of particles, Volume, and Temperature)…
