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.
How to start a QM/MM study from a Molecular Dynamics (MD) simulation? [See Tutorial]
Operating System: macOS, Linux, or Windows.
Visual Molecular Dynamics (VMD) 1.9.3 (Free Download) or later.
Alternatively, you could install molUP manually:
- Download or Clone the repository.
- Copy the molUP directory to a location on your computer. (Get that location!)
- Copy the text inside “install.txt” file and paste on your .vmdrc file (macOS and Linux ) or vmd.rc file (Windows).
- Replace the string “$::vmdStorePath/plugins/molUP” by your installation location (Step 2).
- Save the .vmdrc or vmd.rc file.
- Restart VMD.
(Optional) Run molUP from bash
molUP supports now the loading of Gaussian files directly from your command line (available for macOS and Linux).
- Add the following line to your .bashrc (Linux) or .bash_profile (macOS) file. (This file is located in the HOME directory) You have to edit the “path of the bashScript.tcl file” field by the complete path of this file that is located in the molUP installation directory: “molUP/lib/bashScript.tcl”
alias molUP='vmd -e "path of the bashScript.tcl file" -args'
- Call molUP from the command line:
Open a Gaussian file using the standard procedure:
molUP "Gaussian file"
Open a Gaussian output file reading all available structures:
molUP "Gaussian file" -all
If you experienced any type of issue, please contact us to fix it as soon as possible. (Provide the error message and the file that causes it.)
If you have any idea of new features, please let us know to try the implementation in a future version.
If you used molUP, please cite