Installation

Download, unzip, and run.

This program doesn't require an installation; it's downloaded and launched as a standalone executable. On Windows, extract the downloaded archive, and move the folder to a location of your choice. For example, C:\Program Files\molchanica. Run by double-clicking molchanica.exe. You may pin to the task bar or start menu as desired for your workflow. Windows will automatically find the application when searching using the Windows key.

The files in the archive vary slightly by operating system. For example, the Linux version includes a shell script for setup on the Gnome GUI. The versions with GPU support also include a CUDA FFT library file. The Linux version includes a standalone icon file, while the Windows one embeds this in the application. The Readme is included in downloads. Below is an example archive contents:

Linux setup script

On Linux, how you launch depends on your distribution. You may launch it directly from CLI, but some distros don't allow double-clicking from the GUI. On Gnome distributions (Like Ubuntu and Debian), run setup_linux_desktop.sh, packaged with the executable. This creates a Desktop entry, which allows the program to be pinned to the side menu, or launched from search. Don't run this with sudo, or it won't be able to create the Desktop entry.

We provide two types of downloads: Ones marked _nocuda, and ones without. The ones not marked as _nocuda are much larger due to the inclusion of CuFFT (see below). If you have an Nvidia GPU, download the normal archive. If not, download the _nocuda one.

If you have a Linux distribution which the download is not compatible with, let us know. You may wish to compile from source. For details on this, see the Readme file in the source code, but bottom line: Install the Rust compiler, and run cargo build --release in the project directory.

Gemmi bundling

This application optionally uses the Gemmi CLI program to open some electron density formats like MTZ, and 2fo-2fc mmCIF files. Gemmi must be next to the application, or on the Path to support these file types. We bundle directly with the application on Windows. (Keep it in the same folder as the executable). On Linux, the installation script will load it from apt.

Other linux distributions

If you're running a Linux distribution that does not have a compatible API with Ubuntu and Debian, you can compile from source. Compile from source by downloading and installing Rust, then running cargo build --release from a CLI in the project directory. See notes in the compiling section below about setting up Amber parameter files, and either installing the CUDA toolkit, or disabling CUDA.

CuFFT library

If using CUDA for long-range reciprical forces, we currently require the cuFFT library to be available. Unlike for normal CUDA and 3D graphics, this requires more than an Nvidia graphics driver; it requires libcufft.so.12 (Linux), or cufft64_12.dll (Windows). We provide this library with the application. It must be available either on the system PATH or LD_LIBRARY_PATH environment variables. On Windows, it may also be placed in the same directory as the Molchanica executable. The Linux setup script places it in the appropriate location.

GROMACS and ORCA integration

These integrations are optional, and they're not required to use core Molchanica functionality. To use our integration with these MD and quantum chmistry engines, you must install GROMACS or ORCA separately. See their official installation guides for details, and see the relevant docs sections here, and for those projects. These applications must be available on the system Path environment variable for Molchanica to recognize them.