Installation

Download, unzip, and run.

Molchanica can be launched directly after downloading an unzipping, or placed somewhere suitable using the setup script for your operating system. Extract the downloaded archive, and run molchanica.exe (Windows) or molchanica (Linux). Setup scripts are included for both operating systems, and are optional: they move the program to a standard location, and create a Start menu or desktop entry. See Setup scripts below.

However you install, Molchanica keeps everything it writes in the folder its executable is in, rather than scattering data across the OS's per-user locations. See the data folder section for the layout, and for what this means when choosing where to put the program.

The files in the archive vary slightly by operating system. Each includes a setup script. 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:

Setup scripts

Both setup scripts install for the current user only, so neither needs administrator or root rights. This is deliberate: it's what lets the program write its preferences, downloaded molecules, and installed tools into its own install folder.

On Windows, run setup_molchanica.ps1 — or double-click setup_molchanica.bat, which runs it without requiring a change to your PowerShell execution policy. It moves the program to %LOCALAPPDATA%\Programs\Molchanica (that is, C:\Users\<you>\AppData\Local\Programs\Molchanica), brings along the bundled Gemmi and cuFFT files if your download included them, and creates a Start menu shortcut. Windows will then find the application when you search using the Windows key, and you may pin it to the task bar as desired for your workflow. The first time you run the program, you may get the message "Microsoft Defender prevented an unrecognized app from starting"; click More info, then Run Anyway. A similar obstacle may be encountered on Windows: If it refuses to launch, with an error about "Smart App Control", you may disable "Smart App Control" in Windows Settings.

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_molchanica.sh, packaged with the executable. This moves the program to ~/molchanica, and 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 it directly with the application on Windows, in a gemmi/ folder; keep that folder in the same folder as the executable. The Windows setup script copies it across for you. On Linux, install it from your package manager, e.g. sudo apt install gemmi.

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 Windows setup script does this for you. The Linux setup script likewise copies libcufft.so.12 into the install folder, next to the binary.

External tool integration

External tools aren't bundled directly with Molchanica; they can be managed from the Tools window