MIPET (Mesoscopic Interaction Parameter Estimation with Tinker) is an open-source software project that calculates non-bonding intermolecular interaction energies and determines coordination numbers. The results of these calculations are used by MIPET to generate a "particle set" for the execution of a Dissipative Particle Dynamics (DPD) simulation. Tinker tools are utilized for computing both interaction energies and coordination numbers.
The "src" subfolder contains all source code packages.
The tests can be found in the "test" subfolder.
The "testdata" subfolder contains the necessary files and data to test the pipeline.
The "resources" subfolder contains all code resources.
The "MIPET.job" file is the file to configure a calculation job.
The Molecules subfolder contains Tinker .xyz files for different molecules for the force fields AMOEBA09, MM3, MMFF, OPLSAA and SMOOTHAA as well as their SMILES codes in the SMILES subfolder. The Tinker .xyz file is the basic Tinker file type for Cartesian coordinates. After a tile line it contains one line for each atom in the structure. Each atom respectively its line contains the sequential number within the structure, an atomic symbol or name, X-, Y-, and Z-coordinates, the force field atom type number of the atom, and a list of connected atoms [Tinker guide]. To create a new Tinker .xyz file a mol file of the molecule can be transformed into a Tinker .xyz file using the Tinker tool mol2xyz. The corresponding force field atom type numbers of the atoms must be added manually. A more detailed instruction can be found in the Tutorial.
The subfolder Mathematica notebooks for visualization includes multiple Mathematica notebooks designed to aid in evaluating and visualizing the results of the pipeline. Each notebook includes a short introductory tutorial on its usage. It is important to note that a licensed version of Mathematica 13 (or higher) is required to use these notebooks.
The "Tutorial" folder contains a detailed tutorial on how to install and use MIPET, together with tutorial job files.
The subfolder Publication 2024 contains supplementary and supporting materials for our forthcoming article on the calculation pipeline, set to be published in 2024.
The subfolder C10E4-water bilayer formation study contains a bunch of job files for DPD simulations performed with MFsim. Detailed information can be found in our scientific articles, that will be published 2024.
The subfolder Gaussian job files contains a bunch of job files for DFT calculations that were carried out as part of the development of MIPET using Gaussian. Detailed information can be found in our scientific articles, that will be published 2024.
The Legacy subfolder contains legacy source code and files which were developed as part of the development of MIPET.
Pre-compiled and executable MIPET distributions can be found attached to the marked releases.
Windows:
A convenient Windows OS installer executable for MIPET is available
(click here
to automatically download the installer .exe of the latest version). Download the installer .exe, start, and follow the
instructions to install MIPET. Note that the installation includes a full Java Runtime Environment (JRE). A more
detailed instruction can be found in the Tutorial.
Linux:
Every release has a zip file attached which contains the MIPET Java archive with all dependencies (except Tinker) and a
full Java runtime environment
(click here
to automatically download the zip file of the latest version). A more detailed instruction can be found
in the Tutorial.
In order to run MIPET, the Tinker molecular modeling tool package has to be added. For this, the Tinker executables and
the files for the atomic parameters of version 8.10.2 must be downloaded
(click here to go to the Tinker website). Choose the correct version for
your OS. The atomic parameters can be found in the "Tinker Package Distribution" archive.
Inside is a directory named "params" in which all atomic parameter sets can be found.
Please note the current licence.
The executables and the parameter files have to be placed in a subfolder named "tinker", which you have to create in the
root directory of MIPET.
A more detailed instruction can be found in the Tutorial.
Example directory structure:
├── MIPET # MIPET root directory
│ ├── ...
│ ├── tinker # Tinker directory
│ │ ├── params # Directory to put parameter files
│ │ ├── alchemy.exe # Tinker executable
│ │ ├── analyze.exe # Tinker executable
│ │ └── ... # more Tinker executables
│ └── ...
- Java Development Kit (JDK) version 21
- AdoptOpenJDK (as one possible source of the JDK)
- Chemistry Development Kit (CDK) version 2.9
- Tinker - Software Tools for Molecular Design version 8.10.2
- JUnit version 4.13.2
- Apache commons-lang3 version 3.12.0
- Felix Baensch
- Mirco Daniel
- Veit Hucke
- Achim Zielesny
- Christoph Steinbeck
Zielesny Research Group
Westphalian University of Applied Sciences
August-Schmidt-Ring 10
D-45665 Recklinghausen Germany