Atom: a MATLAB library for creating discrete or periodic systems and topologies (for Gromacs)

Third party tools and files
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The purpose of the atom MATLAB library (>100 functions) is to automate and enable construction (adding solutes, solvent molecules without molecular overlap) of especially solvated inorganic multicomponent molecular systems, by generating system configurations, topological information and Gromacs input files with bonds, angles and dihedrals stretching over PBC. It is hence ideal for periodic custom systems such as layered particles. Atomtype assignment according to the forcefields Clayff and Interface FF (both in original and modified flavours…) is generally supported.

Find out more at:
moleculargeo.chem.umu.se/codes/atom-scripts/ or see this paper detailing the MATLAB library.

Or just download at:
Matlab Filexchange (preferred) | GitHub

Contact: Michael Holmboe, michael.holmboe@umu.se

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Hi again,

I have just released a ChatGPT-based tutor for the ATOM MATLAB library (a so-called GPTs, requires chatgpt plus to access), that seem pretty helpful. It does not always get things right, but is overall quite impressive in its capabilities.
ATOM-library-tutor

/Michael Holmboe