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molUP

Operating systems: MacOS and Linux.

Contacts : Henrique Silva Fernandes Maria João Ramos Nuno Sousa Cerqueira

1. Introduction

molUP is a VMD extension that provides a simple manner for loading and saving Gaussian files, and analyze related results. molUP provides a graphical interface for VMD where the users can load and save chemical structures in the Gaussian file formats. This extension includes a set of tools to set up any calculation supported by Gaussian, including ONIOM; analyze energies through interactive plots; animate vibrational frequencies; draw the vectors associated with those frequencies; modify bonds, angles, and dihedrals; and collect bibliographic information on the employed methods.

Main Features:

Load Gaussian Input (.com) and Output files (.log) on VMD;
Assign ONIOM layers (High-, Medium-, and Low-level);
Select free and fixed atoms during geometry optimization (Freeze status);
Analyze and edit atomic charges;
Setup new Gaussian calculation using the Gaussian input section;
Load scan across reactional coordinates and plot the structure's energies;
Load Gaussian frequency calculations, animate the vibrational modes and show respective vectors;
Show quick useful representations such as the protein, the different ONIOM layers, and the fixed atoms;
Structural Manipulation: adjust the bond length, angle amplitude, and dihedral angle torsion;
Provide a complete bibliographic list of references according to the type of methods and functionals that were employed in the calculation;
Among others.