[gmx-users] GROMACS in Windows Command Prompt

George Tsigaridas gtsig at upatras.gr
Thu Sep 3 16:51:32 CEST 2009

OK Mark. But at least, I wonder if the use of the command prompt is going to 
make easier the application of MPI in a PC network running Windows XP (see 
also my previous message). What's your opinion?



----- Original Message ----- 
From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, September 03, 2009 5:20 PM
Subject: Re: [gmx-users] GROMACS in Windows Command Prompt

> 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
> systems.
>>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
> http://oldwiki.gromacs.org/index.php/Installation#Getting_access_to_GROMACS_after_installation
>> 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.
> Mark
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