Re: [gmx-users] GROMACS in Windows Command Prompt
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? Thanks George - Original Message - From: "Mark Abraham" To: "Discussion list for GROMACS users" 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 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php No virus found in this incoming message. Checked by AVG - www.avg.com Version: 8.5.409 / Virus Database: 270.13.76/2342 - Release Date: 09/02/09 18:03:00 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] GROMACS in Windows Command Prompt
Hi all I use GROMACS 4.0.4 installed on a Windows XP machine through the Cygwin shell. I have just discovered that if I add the variable "GROMACS" with variable value "...path\GROMACS" 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. 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. I am waiting for your feedback George Tsigaridas___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
