However, I did not test that WSL environment can perform GPU computation in GROMACS. If you are interested in this topic, please check the NVidia homepage. Update: In the developer version of Windows 10, WSL 2 provides CUDA environment. If you don't need the CUDA environment, or CUDA environment is working properly in the Cygwin or WSL, you can just follow up the "Quick and Dirty Installation" described in GROMACS hompage) (I am not sure that Cygwin or WSL can use the Windows' CUDA environment or GPU driver.
Software is created and maintained by Laboratory of Biomolecular Systems Simulation at University of Gdansk.This document briefly introduces how to intsall the GROMACS in Windows without Cygwin or Window subsystem for Linux (WSL), by using Visual Studio: "Native" environment, which is enable to use GPU (CUDA) computation. This software (including its Debian packaging) is available to you under the terms of the GPL-3, see "/usr/share/common-licenses/GPL-3". Improvements in GROMACS plugin for PyMOL including implicit solvent simulations and displaying results of PCA analysis Tomasz Makarewicz, Rajmund Kaźmierkiewicz Journal of Molecular Modeling May 2016, 22:109 License Molecular Dynamics Simulation by GROMACS Using GUI Plugin for PyMOL Tomasz Makarewicz and Rajmund Kaźmierkiewicz Journal of Chemical Information and Modeling 2013 53 (5), 1229-1234 In order to take advantage of latest features you will need to have ProDy library installed and PLUMED compiled into GROMACS.
Download latest plugin version from link: and unpack it.
DBUILD_SHARED_LIBS=off -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/cygdrive/c/ Follow the standard compilation, installation and testing instructions to build, compile and install GROMACS 2016.3 under Cygwin.
Sudo add-apt-repository ppa:makson96/dynamics The easiest way to install the plugin is to use PPA repositories: In this section we will describe the most common. There are at least few ways to install the plugin. Note that exact instruction of how to use program is in the software manual, which is available together with the plugin.
Plugin use the same graphic libraries as PyMOL, so working PyMOL and GROMACS installations are enough to make plugin work. Feel free to modify any component of the stack.