While minimizations of several discrete structures using through-space forces may look correct, please understand the theory behind the force field you are using and that any force field not specifically developed or parameterized for intermolecular forces will not lead to experimentally accurate coordinates. Please note, while you are able to optimize the entire scene, most force fields are not parameterized for multiple discrete molecular structures, and you will be relying on the through-space forces defined in the force field (mainly van der Waals and electrostatic), if defined at all. To do this, you can change the optimization scope to optimize the entire scene. Audience Professionals or students who need a drawing solution for 2D chemical drawing, publishing and informatics About ChemDoodle ChemDoodle 2D contains thousands of chemistry features, helping you produce the highest quality graphics and saving you hours of work. However, you may wish to optimize several discrete molecular structures at the same time and in relation to each other. ChemDoodle is available for Windows, Mac and Linux. ChemDoodle 3D therefore will optimize molecular structures separately and individually as you are editing them. Most small molecule force fields are optimized for describing individual discrete molecular structures.
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