I think you're dealing with a really frustrating issue where your GROMACS simulations are freezing after several hours, even though everything else on your system seems to be running fine. Since you've already updated GROMACS and checked some basics like NVIDIA-SMI, let's dive into a few more potential solutions that might help you get to the bottom of this.

1. Keep an Eye on Temperature:

- Overheating Check: Make sure your GPUs and CPUs aren’t getting too hot. Overheating can cause all sorts of issues. You can use tools like `nvidia-smi` for your GPUs and `lm-sensors` for your CPUs to monitor temperatures while the simulation runs.

- Cooling System: Double-check that your cooling system is working properly. Dust or poor ventilation can cause components to overheat and behave unpredictably.

2. GPU Utilization:

- Monitor Activity: Use `nvidia-smi` to see if your GPUs are actually being utilized during the simulation. If they’re not busy, there might be something preventing GROMACS from accessing the GPUs effectively.

- Check for Errors: Sometimes, `nvidia-smi` will show if there are any errors or warnings related to your GPUs. It’s worth checking to rule out hardware issues.

3. System Logs:

- Look for Clues: Your system logs (`dmesg` and `/var/log/syslog`) might contain hints about what’s going wrong. Errors or warnings that pop up around the time your simulation hangs could point you in the right direction.

4. Power Settings:

- PowerMizer Mode: Try setting PowerMizer to `Prefer Maximum Performance` instead of `Auto`. Sometimes, automatic power management can cause issues during intensive tasks like MD simulations.

5. Compatibility Checks:

- GROMACS and CUDA: Make sure your GROMACS version is fully compatible with the CUDA version you’re using. Incompatibilities between software versions can lead to unexpected behavior.

- Driver and CUDA Versions: Confirm that your CUDA and NVIDIA driver versions play nicely together. If there’s a mismatch, it could cause instability.

6. Stress Tests:

- Test Your GPUs: Run stress tests on your GPUs to check for any underlying hardware issues. Sometimes problems only show up under heavy load.

- Regular Monitoring: Use commands like `nvidia-smi --query-gpu=temperature.gpu --format=csv` to keep tabs on GPU temperatures while your simulation is running.

7. Known Issues:

- Community Help: Check GROMACS forums and documentation for any known issues with your setup. You’re probably not the first to run into this, and someone might have found a solution.

- Latest Updates: Make sure you’re using the most up-to-date version of GROMACS that’s compatible with your system. Sometimes newer versions have important fixes.

8. Lighten the Load:

- Try Fewer Threads: Run the simulation with fewer CPU threads or on a single GPU to see if that helps. Overloading the system can sometimes cause it to freeze.

9. Simplify the Test:

- Small Simulations: Run a smaller or simpler simulation to see if it still hangs. If a simpler setup works, the issue might be with your specific simulation parameters.

10. File System Health:

- Check Disk Space: Make sure your disk isn’t running out of space and that there are no issues with the filesystem. Disk problems can sometimes cause hangs.

If the issue continues, it might be worth reaching out to the GROMACS community or support with all the details. They can often offer insights, especially if it’s something others have encountered. Hopefully, one of these steps will help you get your simulations running smoothly again!

Dear Nikhil Kumawat,

Thank you for your detailed response and suggestions. I have tried most of the methods you recommended, but unfortunately, none of them have resolved the issue. I also checked various forums, and so far, I've only found one similar question posted by someone else, but it hasn't received any responses either.

I will continue exploring other options to find out the cause.

Thank you once again.

The issue could be related to system resource exhaustion, GPU temperature throttling, or memory issues. Try the following steps:

All of which can be easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.