Dear Cosmas O. Okoro

I think it is pretty hard to just give a general answer. If you never used GROMACS, this is a good starting point

http://www.mdtutorials.com/gmx/

Start from tutorial 1 which gives examples of file to run GROMACS simulations, and then move to 5 that is the protein-ligand complex. The first one will give you an idea of how to manage runs in general, I think there you willfind most answers and .mdp file examples, which are the files where you tell GROMACS what to do.

Hope this helps,

Nicola

GROMACS 4.5.6 is an outdated version. Please consider using the latest version.

Video Tutorial of the protein-ligand complex for beginner:

https://www.youtube.com/watch?v=PCsg4rBN6wg

https://www.youtube.com/watch?v=lBT404qVBSY

https://www.youtube.com/watch?v=fSDD6tEEWlo

MD tutorial:

http://www.mdtutorials.com/

Hope you can find it helpful!

Dear Cosmas O. Okoro

Fist of all Suparna Ghosh is right, install the latest version. There have been some updates, especially in commands, so better stick to the most update one.

I never installed it on windows. If you have a workstation where you plan to launch the simulations then you create a partition and install some Ubuntu version (18.04 or 20.04 LTS should work fine) or try to install the Ubuntu subsystem in win10 (https://www.windowscentral.com/install-windows-subsystem-linux-windows-10). I run simulation on a cluster but most of the times I do analysis locally in the ubuntu subsystem, which is great if you can't install ubuntu directly on your machine.

I think you can install it on windows and maybe there are some tutorial around, but I can't help you with that since I never tried. By looking at older questions here in researchgate (like this one https://www.researchgate.net/post/I_need_to_install_GROMACS_on_windows_10_64_bit_system_Can_anyone_help_me_with_a_step_by_step_tutorial) it seems better to proceed like I said (install Ubuntu 18.04 LTS in WIN10 e then GROMACS in the ubuntu subsytem).

Hope this helps,

Nicola

If you want to use GROMOS forcefields for protein and Ligand forcefield from ATB server, then follow this protocol:

https://www.protocols.io/view/molecular-dynamics-md-simulations-step-by-step-pro-mztc76n

http://www.mdtutorials.com/gmx/