Made tutorial slightly less confusing.

Change-Id: Ief3132a54770e8b3c3b69b24b5582ba321ccc5fd

diff --git a/share/html/online/getting_started.html b/share/html/online/getting_started.html
index 487001680113d8ec8c1bde7a84012e481b1dc6e4..99997cf497e3cf3770d42ad7e8f0b7f3479edc02 100644 (file)
--- a/share/html/online/getting_started.html
+++ b/share/html/online/getting_started.html
@@ -97,12 +97,10 @@ luck: command not found.
 then you have to verify where your version of GROMACS is installed.
 
 In the default case, the binaries are located in
 then you have to verify where your version of GROMACS is installed.
 
 In the default case, the binaries are located in

-'/usr/local/gromacs/<arch>/bin', where <arch> is the
-architecture of your computer. However, you can ask your local system
+'/usr/local/gromacs/bin', however, you can ask your local system

 administrator for more information.  If we assume that GROMACS is
 administrator for more information.  If we assume that GROMACS is

-installed in directory <tt>XXX</tt> and your machine architecture is
-<tt>sgi</tt> you would find the executables (programs) in
-<tt>XXX/sgi/bin</tt>.  To be able to access the programs without
+installed in directory <tt>XXX</tt> you would find the executables (programs) in
+<tt>XXX/bin</tt>.  To be able to access the programs without

 problems, you will have to edit the login file for your shell. If you
 use the C shell, this file is called <TT>.cshrc</TT> or
 <TT>.tcshrc</TT>, and it is located in your home directory. Add a line
 problems, you will have to edit the login file for your shell. If you
 use the C shell, this file is called <TT>.cshrc</TT> or
 <TT>.tcshrc</TT>, and it is located in your home directory. Add a line


@@ -114,7 +112,7 @@ like:
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt> 
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 <tt> 

-setenv PATH "XXX/&lt;arch&gt;/bin:${PATH}".
+source XXX/bin/GMXRC

 </tt>
 <td></td>
 </tr>
 </tt>
 <td></td>
 </tr>


@@ -123,10 +121,27 @@ setenv PATH "XXX/&lt;arch&gt;/bin:${PATH}".
 
 Issue this command at the prompt too, or log off and on again to
 automatically get the environment.
 
 Issue this command at the prompt too, or log off and on again to
 automatically get the environment.

+You should have an environment variable set now that is called
+GMXDATA that we will use further on. Let us check whether this was
+successful using:<br><br>
+
+<table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
+<tr NOSAVE>
+<td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
+<td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
+
+<tt> echo $GMXDATA
+</tt>
+<td></td>
+</tr>
+</table>
+<br>
+If it prints a directory name you are ready to rock, otherwise go back two steps.

 
 <P><H3><A NAME="examples">Examples</A></H3>
 Before starting the examples, you have to copy all the neccesary
 
 <P><H3><A NAME="examples">Examples</A></H3>
 Before starting the examples, you have to copy all the neccesary

-files, to your own directory. Chdir to the directory you want to put
+files, to your own directory, let us call it work. 
+Mkdir and chdir to the directory you want to put

 the examples directory. This directory (named <tt>tutor</tt>) 
 will need
 about 20 MB of disk space, when it is completely filled.<br><br>
 the examples directory. This directory (named <tt>tutor</tt>) 
 will need
 about 20 MB of disk space, when it is completely filled.<br><br>


@@ -135,7 +150,7 @@ about 20 MB of disk space, when it is completely filled.<br><br>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 

-<tt> cd "your own directory"
+<tt> mkdir work; cd work

 </tt>
 <td></td>
 </tr>
 </tt>
 <td></td>
 </tr>


@@ -147,13 +162,13 @@ then copy the examples: <br><br>
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 
 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 

-<tt> cp -r XXX/share/tutor .
+<tt> cp -r $GMXDATA/gromacs/tutor .

 </tt>
 <td></td>
 </tr>
 </table>
 <br>
 </tt>
 <td></td>
 </tr>
 </table>
 <br>

-(NOTE: include the "<TT>.</TT>", and replace <tt>XXX</tt> by the real directory)<br>
+(NOTE: include the "<TT>.</TT>")<br>

 If that directory doesn't exist you could look for the files
 in <tt>/usr/local/share/gromacs/tutor</tt>, or ask your local GROMACS expert.
 <br> You now have a subdirectory
 If that directory doesn't exist you could look for the files
 in <tt>/usr/local/share/gromacs/tutor</tt>, or ask your local GROMACS expert.
 <br> You now have a subdirectory