What version of Modeller is better to use under Cyg win on 64 bit
Windows system? I have problems while using the Windows version of
the program.
No version of Modeller will run under Cygwin (except the Windows version
of course, but that's not using the Cygwin environment). Cygwin allows
Linux source code to be compiled on a Windows system, but doesn't let
you run Linux binaries. If you want to do that, check out something like
VMWare or VirtualBox.