Dear Harindu,

How are you starting Namd2?

Namd2 does not possess a graphical interface, and therefore shouldn't be launched by double clicking to run it.

Instead, it needs to be run from the command line, specifying the name of the NAMD configuration script you're trying to run, like below:

"Namd2.exe your_config_file.namd"

Hope this helps,

Patrick

Additionally, as a tip for when you're running the simulation. If you want the output energies and errors to be written to a file instead of the command prompt, run:

"Namd2.exe your_config_file.namd > your_output_file.out"

Patrick Timmons I tried lunching namd2 using above mentioned command but failed to execute. The only way I was able to fix the issue was by reformating the computer.

That's strange, sounds like the problem was with Windows. Glad you fixed the problem though.

Patrick Timmons thank you for your attention