Is there a Windows-based molecular dynamics simulation software which is easy to use?
LAMMPS provides pre-compiled Windows binaries. You can download them here.
Instructions for installing GROMACS on Windows (even if you don't want to use Cygwin!) are here.
- Free, and open-source.
- Long history: First released in 1991, based on an earlier program called GROMOS from 1978.
- Under very active development: For many codes, the majority of the development was done years or decades ago, but the development of GROMACS seems only to have grown, not waned. Last year (2019) seems to have been the most active year of development so far!
- Since the very beginning (decades ago), it was designed to run in parallel (i.e. fast). It now also supports GPUs.
- According to Steve Plimpton, a fator of 2x speed-up in GROMACS compared to LAMMPS is "not surprising" because GROMACS has pairwise interactions implemented in assembly code. Therefore GROMACS might be the fastest free MD code.
- It is primarily a classical MD code, so quantum effects are not the focus. QM/MM is possible, but seems to involve interfaces with other codes such as GAMESS, GAUSSIAN, or CPMD. Codes like DFTB+ and BigDFT might be better when quantum effects are important.
On their own website, they say:
"It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions, but [...] many groups are also using it for research on non-biological systems, e.g. polymers."
So it's certainly possible to run GROMACS for non-biological systems, but it's not their focus.
Run any Linux program on WSL (Windows Subsystem for Linux)
One interesting alternative is using the Windows Subsystem for Linux (more info at: https://docs.microsoft.com/en-us/windows/wsl/install-win10 ). I know of successful cases where this has been used to install GROMACS (recent versions). I don't have a reason to believe it wouldn't work for other MD software as well. It also has a way of using the GPU with CUDA as in https://developer.nvidia.com/cuda/wsl
Definitely something worth trying, it should be easy enough and we all know how Cygwin can be a pain to setup sometimes.
This would've been a comment if I had enough votes to comment :).
OpenMM is a highly efficient molecular dynamics package which can run via Python. Therefore, any way you normally run python can work. For example, via a Jupyter (Ipython) notebook, via a python GUI, Window's PowerShell, Window's subsystem for Linux, etc.
You can download OpenMM via the python manager Anaconda, which makes it very easy to install. For example,
conda install -c omnia openmm
OpenMM, however, is not an input/output type of program but is directed completely through python code. This is also known as an Application Programming Interface (API).
This is good because you know exactly what is going on and have more finer control. But that also does require you know what you're doing more. There are several code bases out there that attempt to create easier "wrappers" around the python. For example, see https://github.com/leeping/OpenMM-MD
Run any Linux program from Windows using Cygwin
If you really need running Molecular Dynamics on Windows, you can use Cygwin and port your code from Linux to Windows. Using this, you can test some on them and select which one is easier for you (as it is a personal issue). Be aware that their performance will be drastically affected as Linux is more efficient running jobs (distributing among cores and using memory) than Windows.
A MD simulation software which can run any system but has been particularly developed for the target audience that study biomolecular systems (proteins, lipid bilayers, etc.)
They have multiple pre-compiled versions for running in Windows machines, including versions that can be used in HPCs and GPU based accelaration using CUDA. (You can download CUDA toolkit for Windows from here)
- Win64 (Windows 7, 8, 10, etc.)
- Win64-CUDA (NVIDIA CUDA acceleration)
- Win64-MPI (Windows HPC Server, multi-copy algorithms)
- Win64-MPI-smp-CUDA (HPC Server with CUDA)
You can download these different binaries from here, they're free to use for academic users.
They also have a nice tutorial for starting and running simple MD simulation for their Windows version of NAMD.
The visualization software VMD is also developed by the same group and therefore NAMD has multiple functionalities that can be availed through VMD - like running a MD simulation, analysing MD trajectories from NAMD etc.