From: David van der Spoel Date: Tue, 4 Sep 2012 13:27:57 +0000 (+0200) Subject: Made tutorial slightly less confusing. X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=ffb176aee364c74dd86021179fe9d371aed464e3;p=alexxy%2Fgromacs.git 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 4870016801..99997cf497 100644 --- 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 -'/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 -installed in directory XXX and your machine architecture is -sgi you would find the executables (programs) in -XXX/sgi/bin. To be able to access the programs without +installed in directory XXX you would find the executables (programs) in +XXX/bin. 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 .cshrc or .tcshrc, and it is located in your home directory. Add a line @@ -114,7 +112,7 @@ like: -setenv PATH "XXX/<arch>/bin:${PATH}". +source XXX/bin/GMXRC @@ -123,10 +121,27 @@ setenv PATH "XXX/<arch>/bin:${PATH}". 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:

+ + + + + + +
+ + echo $GMXDATA + +
+
+If it prints a directory name you are ready to rock, otherwise go back two steps.

Examples

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 tutor) will need about 20 MB of disk space, when it is completely filled.

@@ -135,7 +150,7 @@ about 20 MB of disk space, when it is completely filled.

- cd "your own directory" + mkdir work; cd work @@ -147,13 +162,13 @@ then copy the examples:

- cp -r XXX/share/tutor . + cp -r $GMXDATA/gromacs/tutor .
-(NOTE: include the ".", and replace XXX by the real directory)
+(NOTE: include the ".")
If that directory doesn't exist you could look for the files in /usr/local/share/gromacs/tutor, or ask your local GROMACS expert.
You now have a subdirectory