Hi Rohit Kunar

I assume you're referring to protein simulations in water rather than protein-ligand simulations. Currently, WebGro does not support protein-ligand simulations.

The choice of a simulation tool depends on the duration you need. If you're looking for a short simulation, you can use Visual Dynamics web browser (https://visualdynamics.fiocruz.br/en-US), which allows simulations up to 5 ns. However, in most cases, 5 ns is insufficient to assess protein stability over time.

For extended simulations, GROMACS is a better option. It offers excellent documentations of different types of simulations (protein-ligand, protein in water, umbrella sampling etc to name a few), in-built analysis tools, an active community, and expert support, making it way more easier to troubleshoot issues and perform molecular dynamics simulations.

If you’re looking to run molecular dynamics (MD) simulations for large protein structures, like those generated by AlphaFold, Here are some options to consider:

1.CHARMM-GUI

This is a user-friendly, web-based platform that helps you set up and run MD simulations. It works well with large systems and integrates seamlessly with popular MD engines like CHARMM, NAMD, GROMACS, and AMBER.

Check it out here: [CHARMM-GUI](https://www.charmm-gui.org)

2.GROMACS Online

If you’re a fan of GROMACS, this cloud-based service is perfect for running simulations on large protein structures. It even offers pre-configured workflows to make your life easier.

Visit their site: [GROMACS](https://www.gromacs.org)

3. **AMBER MD Web Portal**:

AMBER’s web interface is another excellent choice for running MD simulations on large systems. It also provides handy tools for preparing and analyzing your structures.

Explore it here: [AMBER](https://ambermd.org)

4.HADDOCK

While HADDOCK is mainly known for docking, it also supports MD simulations for large protein complexes. It’s a versatile tool worth checking out.

Take a look: [HADDOCK](https://wenmr.science.uu.nl/haddock2.4)

5.MDWeb

This web-based platform uses GROMACS for MD simulations and is designed to handle large structures. It also offers automated workflows to streamline the process.

Learn more: [MDWeb](https://mmb.irbbarcelona.org/MDWeb)

6.Google Colab with OpenMM

For those who are comfortable with a bit more advanced setup, Google Colab can be a powerful and free option. Using OpenMM, you can run scalable MD simulations for large systems.

These tools should give you options to work with, CHARMM-GUI is great choice Hope it helps :]