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GROMACS interaction models

Publisher: OneAngstrom

Updated: June 10, 2020


Latest versions

Windows: 0.9.7 on SAMSON 0.12.0

Linux: 0.9.7 on SAMSON 0.12.0

Mac: 0.9.7 on SAMSON 0.12.0

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GROMACS interaction models

Publisher: OneAngstrom

Updated: June 10, 2020


Latest versions:

- Windows: 0.9.7 on SAMSON 0.12.0

- Linux: 0.9.7 on SAMSON 0.12.0

- Mac: 0.9.7 on SAMSON 0.12.0

Perform interactive simulations with GROMACS force fields.

This SAMSON Element wraps GROMACS 5.1 force fields and setup tools.

Usage

Use the "GROMACS Model Generator" app (find it in the App menu, or using the Search box in the top right of SAMSON's interface), which generates a structural model suitable for simulation (i.e. add hydrogens, etc.). Then, apply a simulator from the Simulation menu and choose "GROMACS force field" to add a GROMACS interaction model suitable for interactive minimization and simulation (no periodic boundary conditions). You should use the same force field that was used for preparation.

Note that, at the moment, at most one structural model should be selected (or in the document, when the selection is empty), and that bond lengths are not yet constrained in this version.

This may be combined with the Twister editor to perform large-scale modifications of the structure, and the secondary structure visual model for interactively updated secondary structure prediction.

Important: this module is for interactive simulation. If you would like to use GROMACS for non-interactive simulations and perform preparation, minimization, equilibration and simulation runs, you should use the GROMACS Wizard module.