[gmx-users] Editing the log in files [HN]
Justin A. Lemkul
jalemkul at vt.edu
Tue Dec 16 20:15:14 CET 2008
Hideya Nakamura wrote:
> I installed gromacs in Cygwin-related home. Is it correct?
That's fine, as long as you know where it is, but that means you probably
altered something during configuration.
>
> I tried "which luck" command, but I could not find GMXRC in the list of
> executables.
>
Were the other executables there?
> I will try to install gromacs again. Of course, I will learn about
> Gromacs more.
Sounds like a good idea. Leave the --prefix option alone during configuration;
it should default to /usr/local/gromacs.
-Justin
>
>
>
> 2008/12/16 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
> Hideya Nakamura wrote:
>
> Thank you Justin for your prompt response.
>
> I installed Gromacs in the home directory of Cygwin.
>
>
> Is that your home directory, or some Cygwin-related home? I do not
> have my Windows partition up in front of me; I just remember that
> Cygwin's organization is a bit convoluted.
>
>
> Actually, I can't fine the bin subdirectory in the gromacs
> directory.
> (I also can't find GMXRC anywhere.)
>
>
> Did you try "which luck" as I suggested before? That should
> indicate where the executables were installed.
>
>
> Does this mean Gromacs cannot be installed correctly?
>
>
> Not necessarily.
>
>
> Do I have to install gromacs again?
>
>
> What were you *exact* commands through the installation process? If
> you did indeed follow the Cygwin HowTo on the wiki, Gromacs should
> have been installed in /usr/local/gromacs. I doubt that your
> installation is broken, but you'll have serious headaches if you
> don't familiarize yourself with the locations of executables,
> libraries, and force field files.
>
> -Justin
>
>
> Hideya
>
>
> 2008/12/16 Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>>
>
>
>
>
> Hideya Nakamura wrote:
>
> Hello Mark and Justin,
>
> Thank you very much for your responce.
> I edited the .bashrc file which is in my home directory.
> I opened .bashrc file using vi and added "source
> /usr/local/gromacs/bin/GMXRC" at the last line.
> And then, I started Cygwin again. However, an error mesage
> (bash: /usr/local/gromacs/bin/GMXRC: No such file or
> directory)
> is showed when I start Cygwin. In addition, when I enter the
> command "luck" for gromacs, I can't see the correct responce
> (i.e. "Whatever Happened to Pong ?" (F. Black))
> Could you please tell me your suggestion?
> I am using Cygwin on Windows Vista Enterprise.
>
>
> Where did you install Gromacs? The GMXRC script should be in the
> bin subdirectory of whatever prefix you specified during
> configuration. If your environment is finding luck, then try
> "which
> luck" to locate the PATH to Gromacs.
>
> -Justin
>
>
> Hideya
>
>
> 2008/12/15 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
> <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>
> <mailto:Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>>>
>
>
> Hideya Nakamura wrote:
>
> Hello,
>
> I try to install GROMACS using Cygwin on my
> Windows PC.
>
> I have already installed fftw, and then I will install
> GROMACS
> based on a instruction on wiki.gromacs.org
> <http://wiki.gromacs.org>
> <http://wiki.gromacs.org>
> <http://wiki.gromacs.org> <http://wiki.gromacs.org/>
> (http://wiki.gromacs.org/index.php/Cygwin_HOWTO).
>
>
> In this instruction, there is a description "#6
> Edit your
> login
> files to source /usr/local/gromacs/bin/GMXRC
>
> (or manually add /usr/local/gromacs/man to the MANPATH
> and check
> that /usr/local/bin is in the PATH)."
>
> However, I can't edit my log in files. Could
> someone give
> me how
> to edit my log in files by using Cygwin?
>
>
> Probably you're using bash shell, so in your home
> directory, edit
> the file .bashrc and add the line "source
> /usr/local/gromacs/bin/GMXRC" (or as appropriate for
> wherever you
> installed GROMACS), and then open a new shell. This
> way the
> GROMACS
> environment will always be configured right for you.
>
> Mark
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
>
>
> http://www.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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> ------------------------------------------------------------------------
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> http://www.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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> http://www.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-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list