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molup

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molUP

Operating systems: macOS, Linux, and Windows (NEW)

Contacts : Henrique Silva Fernandes Maria João Ramos Nuno Sousa Cerqueira


This page has been moved, the new location is https://github.com/portobiocomp/molUP.

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.

If you have any suggestion of new features, please contact us: henrique.fernandes@fc.up.pt

2. ScreenShots

3. Download

The software was migrated to GitHub. Please, visit https://github.com/portobiocomp/molUP to download molUP (Available for macOS, Linux, and Windows).

4. Installation

The details about the installation can be founded on the GitHub repository: https://github.com/portobiocomp/molUP

molup.1519061415.txt.gz · Last modified: 2018/02/19 17:30 by nuno