[gmx-users] GROMACS in Windows Command Prompt

Mark Abraham Mark.Abraham at anu.edu.au
Thu Sep 3 16:20:38 CEST 2009

George Tsigaridas wrote:
> Hi all
> I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell. 

OK, so *use* the Cygwin shell... there are much easier ways of setting 
environment variables for the Cygwin shells than through the XP control 
panel (though, rarely, this can be necessary). Those easier ways are 
exactly the ones you might need (to learn ) for *nix shells on other 

>I have just discovered that if I add the variable "GROMACS" with variable value "...path\GROMACS" 

That should do nothing at all.

> in the 
> System - Advanced - Environment Variables - User variables section of the control panel and also add the entry "...path\GROMACS\bin" (pointing to the GROMACS binaries) at the path line of the system variables section on the same tab, then I can run GROMACS and its utilities through the command prompt. 

Yes, that's what the path variable is for. Much more effective is 
running a Cygwin shell (the XP command prompt is nowhere near as useful 
as any Cygwin shell) and following the standard practice here 

> I have not yet checked if the output is the same with the one obtained using the Cygwin shell but at least you have an alternative.

There's more to GROMACS life than being able to run the executables. Do 
yourself a favour and try to ignore the fact that you're running on XP 
as much as possible. You want to learn workflows that are transferable 
to other environments, not partially-effective XP-specific workflows.

Also, to save myself some time in the future, you should avoid using 
Windows-specific file editing tools unless you know how to take care of 
line-ending problems yourself with dos2unix. Learn to use vi or emacs 
from a Cygwin shell.


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