AMD64 code is 64-bit Intel - that will not run under Ubuntu for ARM64  vim and gedit run because they have been recompiled by Ubuntu to run on ARM64.

options:

• See if the author has a version that is compiled for ARM64, or provides source code that could potentially be rebuilt on ARM64.
• someone posted a link to an open open-source x64 to ARM translator for Linux (similar to Rosetta on macOS) that may allow your program to run. Might be something to investigate.
• When running on a hypervisor application that supports Apple’s high level virtualization framework (like UTM) Apple has a way to use Rosetta in ARM64 Linux operating systems. That will not work for fusion because it uses a different set of Apple’s frameworks that does not support Rosetta. 

By “VMD”, do you mean the VMD program that is provided by the University of Illinois at Urbana-Champaign? If so, they have an alpha version 1.6.4 that runs natively on Apple Silicon Macs. 

I'm aware of that thank you, I need to use a Linux machine because some other programs don't have a Apple Silicon version.

Thank you for the other reply, I'll look more into the x64 to ARM translator

It's Box64.