Interactive Modeling UFF (IM-UFF)

Introduction We previously proposed ([1]) a new implementation of the UFF interaction model introduced by Rappe et al. in [2], combined with an automatic scheme to perceive the molecular system in order to compute the bonds, bond orders and atoms’ types. If interested, you can read our previous post about this interaction model. This post is about the Interactive Modeling Universal Force Field (IM-UFF) interaction model that was published in [3] and which extends the UFF force field for performing…

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Universal Force Field

Introduction This post presents the basics about the Universal Force Field (UFF) interaction model. This interaction model implements the UFF force fields proposed by Rappe et al. in [1]. It also includes an automatic scheme to perceive the molecular system in order to compute the bonds, bond orders, and atom types, so that UFF can directly be applied on a given molecular system. For more details regarding this UFF  implementation and the approach used to automatically perceive the molecular structure,…

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Programming new force fields

Please, refer to the updated version: Developer guide: Programming new force fields. This tutorial will guide you to create a simple spring model force field such that a virtual spring links two pairs of atoms connected by a covalent bond. Using the Element Generator The first step is to use the SAMSON SDK Element Generator to generate a module where you will implement your force field. Lauch the ElementGenerator. Select the path for your new module, press next. Give a name to…

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Simulating small molecules, graphene and proteins

For more information please refer to User guide: Modeling and Simulation. Note: this tutorial has been made for an older version of SAMSON. Introduction This tutorial will make you perform different types of simulations using various force fields and integrators. In SAMSON, force fields are named Interactive Models and integrators state updaters. Simulations are interactive in the sense that users can still act on the atoms while the simulation is running. First, you need to download the benchmarks available at the…

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