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====== molUP ======


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

[[https://github.com/portobiocomp/molUP|{{:b-download.png?direct&100}}]]

Contacts : [[henrique.fernandes@fc.up.pt|Henrique Silva Fernandes]]  [[mjramos@fc.up.pt|Maria João Ramos]] [[nscerque@fc.up.pt|Nuno Sousa Cerqueira]] 

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===== 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 =====

{{:mm:molup_00001.png?direct&200|}}{{:molup_00002.png?direct&200|}}{{:molup_00003.png?direct&200|}}{{:molup_00004.png?direct&200|}}{{:molup_00005.png?direct&200|}}
===== 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 =====
=== macOS ===
1. Open molUP.dmg.

2. Double click on the icon.
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3. Follow the installation instructions.

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=== Linux ===
1. Untar molUP.tar.
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2. Open the molUP_Installer directory and run the installer ($./molUP).
{{ ::molup_linux00003.png?direct&400 |}}

3. Follow the installation instructions.

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