To utilize the GPUs of your graphics card (GeForce RTX 3060) for molecular dynamics simulations with NAMD2 on Windows 10, follow these steps:

Please note that using GPU acceleration in NAMD requires proper configuration and support from your GPU driver and hardware. Make sure you have the latest GPU drivers installed for your GeForce RTX 3060 graphics card. Additionally, GPU acceleration might not always significantly speed up all types of simulations, so you may need to experiment with different simulation parameters to optimize performance.

Keep in mind that Charmm-Gui typically sets up the simulation parameters for you, so you may need to manually edit the NAMD configuration file to enable GPU acceleration as described above.

Always perform tests and validation to ensure that your GPU-accelerated simulations produce accurate results and match the behavior of CPU-only simulations.

For those who want to conduct MD simulations in Gromacs on a Windows machine, first enable WSL2 in your Windows. Here are some videos/links to help you with WSL2 setup -

Step 1: install Ubuntu 22.04 according to Microsoft's instructions

https://learn.microsoft.com/en-us/windows/wsl/install-manual#step-1---enable-the-windows-subsystem-for-linux

Step 2: refer starting from the 4 minute mark in this video: https://youtu.be/Rzg144v3hfo

Step 3: setting up a shared folder - you can access Windows drives by doing 'cd /mnt/c/' for C drive, or 'cd /mnt/d/' for D drive for example. You can also create a link to a desired folder. Refer video:

https://youtu.be/JgzSVAQjIkY

NVIDIA drivers for WSL2 : https://ubuntu.com/tutorials/enabling-gpu-acceleration-on-ubuntu-on-wsl2-with-the-nvidia-cuda-platform#2-install-the-appropriate-windows-vgpu-driver-for-wsl

Reboot WSL2 after installing NVIDIA drivers

Once you have WSL2 setup, install gromacs like you would on an Ubuntu machine - https://manual.gromacs.org/current/install-guide/index.html

To utilize GPUs while running your simulations on WSL2, or any machine with GPU, make sure this line is included in your MDP file: energygrps = System