Section: New Software and Platforms

SAMSON-GROMACS

Keywords: Algorithm - Materials - Chemistry - Bioinformatics - Structural Biology - Nanosystems - 3D modeling - 3-order

Functional Description: This SAMSON Element wraps GROMACS 5.1 force fields and setup tools. Use the "GROMACS setup" app (in the App menu), which wraps the pdb2gmx tool, to generate 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). 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. Future updates of this SAMSON Element will wrap more GROMACS tools. Source code for this SAMSON Element will be made available at https://gforge.inria.fr/projects/elements/.

• Authors: Stéphane Redon, Minh Khoa Nguyen and Yassine Naimi

• Partner: Inria

• Contact: Stéphane Redon

• URL: http://samson-connect.net