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PACKMOL-GUI

★ 34 Open GitHub ↗

An Integrated VMD Graphical User Interface for Molecular Packing

// repository documentation

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The PACKMOL-GUI was developed utilizing Tcl/Tk, the embedded development interface for VMD extensions. This GUI requires the version 1.9.3 or above of the VMD. Additionally, Furthermore, the PACKMOL-GUI supports the periodic boundary conditions and Gaussian surfaces that were introduced in version 20.15.1 of the PACKMOL program.

INSTALLATION
============
# **1. Download and Extract Files** 
Users can employ auxiliary tools such as DownGit (https://downgit.github.io/#/home), GitZip (https://gitzip.org/) or the GitHub API to download the specific folder. Download options are available for various user needs. 
------------------------------------------------------------------------------------------ 
**Lite‌ Version** 
pakmol1.0 
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**Users of Biomolecular Modeling** 
packmol1.0 
datasets-Biox 
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**Users of Metal-Organic Frameworks Modeling** 
packmol1.0 
datasets-CoRE-MOFs 
_**Note**_: This dataset expands the CoRE MOFs to encompass unit cell dimensions exceeding 2.4 nm and transforms them into PDB format, rendering it suitable for molecular dynamics simulations. The datasets-CoRE-MOFs file is 135 MB compressed and 3.6 GB when extracted. 
To extract CoRE-MOFs-PDB file, use the following commands: 
cat CoRE-MOFs-PDB.tar.xz.part* > temp.xz 
tar -xvf temp.xz 
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To prevent file path issues during installation, it is strongly recommended that users place the **packmol1.0** folder in the **YOUR-VMD-Installation-Directory/plugins/noarch/tcl**. Alternatively, users can choose any location but must use the **lappend auto_path** command to specify the absolute file path.. 
# **2. Installation** 
## 2.1 Manual Installation 
Users are able to install PACKMOL-GUI from any location within the "Extension" menu. However, considering that PACKMOL serves as a modeling tool, it is recommended that users place it under the "Extension/Modeling" submenu for optimal organization and functionality.
Locate the VMD startup configuration file and add the following lines: 
__vmd_install_extension packmol packmol_tk "Modeling/PACKMOL"__ 
The configuration file paths are: 
Windows: YOUR-VMD-Installation-Directory\vmd.rc 
Linux: YOUR-VMD-Installation-Directory/lib/vmd/.vmdrc 
macOS: YOUR-VMD-Installation-Directory/Contents/vmd/.vmdrc 
_**Note**_: If Windows users place packmol1.0 in another folder with spaces, please remember to use the escape character "\\". 
For example, "lappend auto_path C:/Program Files/packmol1.0" should be written as “lappend auto_path C:/Program\ Files/packmol1.0”. 
## 2.2 Automated Installation 
We offer automated installation scripts compatible with various operating systems. Users are required to download the "packmol1.0" directory along with the "install.tcl" script. Please adhere to the instructions outlined below to successfully complete the automated installation process. 
1.	Download "packmol1.0" and "install.tcl". 
2.	Launch VMD. 
3.	Access the directory containing the install.tcl script either through the VMD command-line interface or by navigating to VMD Main -> Extensions -> Tk Console. 
 Write the following command and press ENTER: 
 cd "COMPLETE PATH OF install.tcl DIRECTORY" 
 Example: cd /home/users/ Downloads/PACKMOL-Download 
4.	Write the following command and press ENTER: 
 play install.tcl. 
5.	When prompted, supply the path to the packmol1.0 directory, 
 such as: /home/users/ Downloads/PACKMOL-Download /packmol1.0. 
6.	The installation process will then be completed. Please, re-launch VMD and open PACKMOL-GUI at VMD Main -> Extensions -> Modeling > PACKMOL. 
_**Note**_: On Linux systems, if the installation is conducted with root privileges, it is necessary for the user to specify the path to the .vmdrc file. Compatibility has been evaluated with Windows versions 7, 10, and 11; macOS Mojave version 10.14 (with the caveat that macOS version 10.15 no longer supports 32-bit applications); and CentOS version 7.0 systems. 
**Figure 1.** The interactive and automated procedure for installation.
![config-1](https://github.com/MSM-RAD-X-VMD-Plugin/PACKMOL-GUI/blob/main/annotated-recording-examples/install.gif) 
# 3. Launch VMD 
After starting VMD, you can access the PACKMOL-GUI via the Extensions -> Modeling -> PACKMOL submenu in the VMD Main menu.
# 4. Configuring the PACKMOL Path and Working Directory
Upon successful initialization of the PACKMOL-GUI, it is imperative for users to configure the program path for PACKMOL and establish the current working directory. To achieve this, users should select the "browse" button adjacent to the PACKMOL directory label, navigate to the location of the PACKMOL program, select it, and double-click to finalize the path configuration. For specifying the output file path of PACKMOL, users may click the "browse" button next to the "output directory" label and select an appropriate working directory that aligns with their specific requirements. 
**Figure 2.** Configuring the PACKMOL Path
![config-1](https://github.com/MSM-RAD-X-VMD-Plugin/PACKMOL-GUI/blob/main/annotated-recording-examples/sc-1-Linux.jpg) 
**Figure 3.** Configuring the Working Directory
![config-2](https://github.com/MSM-RAD-X-VMD-Plugin/PACKMOL-GUI/blob/main/annotated-recording-examples/SC-2-Liunx.jpg)

PACKMOL-GUI

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