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.
- 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;
- Add atoms and molecular fragments NEW;
- Remove atoms NEW;
- Among others.
vmdStore provides a user-friendly interface to free install VMD plugins. vmdStore also helps you keeping the plugins always updated.
Google Chrome Extensions
(Sold to “Way2Online Interactive India Pvt. Ltd.” on 2017, November 8th)
See on GitHub