Recent changes to Getting started

Getting started modified by Magnus

Magnus — Fri, 29 Aug 2014 07:24:43 -0000

--- v6
+++ v7
@@ -1,35 +1,35 @@
 Welcome to the Iphigenie molecular dynamics (MD) simulation program.
 To get started follow these steps:

-1. Download the latest version of Iphigenie. 
+1. Download the latest version of Iphigenie
 -------
-Each version subdirectory contains tared and gziped files that can be expanded 
+Each version subdirectory contains tar'ed and gzip'ed files that can be expanded. 

 ~~~~
 :::bash
 tar -xzpvf <filename>
 ~~~~
 from a common _root_ directory.
-Both the 'program' and 'share' files are definately needed. The 'examples' are useful to get an idea what iphigenie provides and how the various features have to be oparated. The latest file 'testsuite' is mainly intended for developers and provides reference output to check if everything runs correctly.
+The 'program' and 'share' files are obligatory. The 'examples' are useful to get an idea what features Iphigenie provides and how they are operated. The last file 'testsuite' is mainly intended for developers and provides reference output for different setups to check if everything runs correctly.

     iphigenie-XXX-program.tar.gz   :   the source code and build system
+    iphigenie-XXX-share.tar.gz     :   parameter and data files
     iphigenie-XXX-examples.tar.gz  :   input file examples
     iphigenie-XXX-testsuite.tar.gz :   reference input and output
-    iphigenie-XXX-share.tar.gz     :   parameter and data files

 2. Compile Iphigenie
 -----
-Follow the [compiling](Compiling) instructions. If in doubt, run the [Test Suite](Test Suite) to verify the numerics of your executable.
+Follow the [compiling](Compiling) instructions. If in doubt about the validity of your build, run the [Test Suite](Test Suite) to verify the numerics of your executable.

-3. Setup the Simulation System
+3. Set up the Simulation System
 -----
-The input files for the MD executable [iffi](iffi) have to be generated from _protein data base_ (.pdb) files and _protein structure files_ (.psf) analogous to [charmm](http://www.charmm.org) and [namd](http://www.ks.uiuc.edu/Research/namd/). You can built these files, for example, with tools provided by the [visual molecular dynamics (vmd)](http://www.ks.uiuc.edu/Research/vmd/) package. Convert these files to the native [iffi](iffi) input format by the [xpl2lis](xpl2lis) tool.
+The input files for the MD executable [iffi](iffi) have to be generated from _protein data base_ (.pdb) files and _protein structure files_ (.psf) analogous to [CHARMM](http://www.charmm.org) and [NAMD](http://www.ks.uiuc.edu/Research/namd/). You can built these files, for example, with tools provided by the [visual molecular dynamics (VMD)](http://www.ks.uiuc.edu/Research/vmd/) package. Convert these files to the native [iffi](iffi) input format by the [xpl2lis](xpl2lis) tool.

 4. Prepare your Control File
 ------
-The [control file](control file) _ctl.xml_ contains the full set of input options and their default settings (follow the [link](control file) for details). For inputs of typical tasks see the [examples](Examples).
+The [control file](control file) _ctl.xml_ contains the full set of input options (follow this [link](control file) for details) and comments. You will only need a small subset of tags for a typical task. For inputs of such tasks see the [examples](Examples).

 5. Run the Simulation
 ------
-Use the [iffi](iffi) executable tu run your simulation. 
+Use the [iffi](iffi) executable to run your simulation.

Getting started modified by Gerald Mathias

Gerald Mathias — Thu, 28 Aug 2014 16:55:03 -0000

--- v5
+++ v6
@@ -22,7 +22,7 @@
 Follow the [compiling](Compiling) instructions. If in doubt, run the [Test Suite](Test Suite) to verify the numerics of your executable.

-3. Setup the Simualtion System
+3. Setup the Simulation System
 -----
 The input files for the MD executable [iffi](iffi) have to be generated from _protein data base_ (.pdb) files and _protein structure files_ (.psf) analogous to [charmm](http://www.charmm.org) and [namd](http://www.ks.uiuc.edu/Research/namd/). You can built these files, for example, with tools provided by the [visual molecular dynamics (vmd)](http://www.ks.uiuc.edu/Research/vmd/) package. Convert these files to the native [iffi](iffi) input format by the [xpl2lis](xpl2lis) tool.

Getting started modified by Gerald Mathias

Gerald Mathias — Thu, 28 Aug 2014 13:22:25 -0000

--- v4
+++ v5
@@ -1,7 +1,7 @@
 Welcome to the Iphigenie molecular dynamics (MD) simulation program.
-To get started follow these steps
+To get started follow these steps:

-1. Download the files provided for the latest version of Iphigenie. 
+1. Download the latest version of Iphigenie. 
 -------
 Each version subdirectory contains tared and gziped files that can be expanded 

@@ -17,16 +17,19 @@
     iphigenie-XXX-testsuite.tar.gz :   reference input and output
     iphigenie-XXX-share.tar.gz     :   parameter and data files

-2. Compile 
+2. Compile Iphigenie
 -----
 Follow the [compiling](Compiling) instructions. If in doubt, run the [Test Suite](Test Suite) to verify the numerics of your executable.

-3. System Setup 
+3. Setup the Simualtion System
 -----
 The input files for the MD executable [iffi](iffi) have to be generated from _protein data base_ (.pdb) files and _protein structure files_ (.psf) analogous to [charmm](http://www.charmm.org) and [namd](http://www.ks.uiuc.edu/Research/namd/). You can built these files, for example, with tools provided by the [visual molecular dynamics (vmd)](http://www.ks.uiuc.edu/Research/vmd/) package. Convert these files to the native [iffi](iffi) input format by the [xpl2lis](xpl2lis) tool.

-4. Control File
+4. Prepare your Control File
 ------
-The [control file](control file) _ctl.xml_ contains the full set of input options and their default settings.
+The [control file](control file) _ctl.xml_ contains the full set of input options and their default settings (follow the [link](control file) for details). For inputs of typical tasks see the [examples](Examples).

+5. Run the Simulation
+------
+Use the [iffi](iffi) executable tu run your simulation.

Getting started modified by Gerald Mathias

Gerald Mathias — Thu, 28 Aug 2014 11:00:06 -0000

--- v3
+++ v4
@@ -24,7 +24,7 @@

 3. System Setup 
 -----
-The input files for the MD executable [iffi](iffi) have to be generated from _protein data base_ (.pdb) files and _protein structure files_ (.psf) analogous to [charmm](www.charmm.org) and [namd](www.ks.uiuc.edu/Research/namd/). You can built these files, for example, with tools provided by the [visual molecular dynamics (vmd)](http://www.ks.uiuc.edu/Research/vmd/) package. Convert these files to the native [iffi](iffi) input format by the [xpl2lis](xpl2lis) tool.
+The input files for the MD executable [iffi](iffi) have to be generated from _protein data base_ (.pdb) files and _protein structure files_ (.psf) analogous to [charmm](http://www.charmm.org) and [namd](http://www.ks.uiuc.edu/Research/namd/). You can built these files, for example, with tools provided by the [visual molecular dynamics (vmd)](http://www.ks.uiuc.edu/Research/vmd/) package. Convert these files to the native [iffi](iffi) input format by the [xpl2lis](xpl2lis) tool.

 4. Control File
 ------

Getting started modified by Gerald Mathias

Gerald Mathias — Thu, 28 Aug 2014 10:58:54 -0000

--- v2
+++ v3
@@ -9,15 +9,24 @@
 :::bash
 tar -xzpvf <filename>
 ~~~~
-from a common directory.
-Both 'program' and 'share' files are definately needed. 'examples' are useful to get an idea what iphigenie provides and how the various features have to be oparated. The latest file 'testsuite' is mainly intended for developers and provides reference output to check if everything runs correctly.
+from a common _root_ directory.
+Both the 'program' and 'share' files are definately needed. The 'examples' are useful to get an idea what iphigenie provides and how the various features have to be oparated. The latest file 'testsuite' is mainly intended for developers and provides reference output to check if everything runs correctly.

-    *   __iphigenie-XXX-program.tar.gz__   :   the source code and build system
-    *   __iphigenie-XXX-examples.tar.gz__  :   input file examples
-    *   __iphigenie-XXX-testsuite.tar.gz__ :   reference input and output
-    *   __iphigenie-XXX-share.tar.gz__     :   parameter and data files
+    iphigenie-XXX-program.tar.gz   :   the source code and build system
+    iphigenie-XXX-examples.tar.gz  :   input file examples
+    iphigenie-XXX-testsuite.tar.gz :   reference input and output
+    iphigenie-XXX-share.tar.gz     :   parameter and data files

 2. Compile 
 -----
-Follow the [compiling](Compiling) instructions. If in doubt, run the [Test Suite] to verify your executable.
+Follow the [compiling](Compiling) instructions. If in doubt, run the [Test Suite](Test Suite) to verify the numerics of your executable.

+
+3. System Setup 
+-----
+The input files for the MD executable [iffi](iffi) have to be generated from _protein data base_ (.pdb) files and _protein structure files_ (.psf) analogous to [charmm](www.charmm.org) and [namd](www.ks.uiuc.edu/Research/namd/). You can built these files, for example, with tools provided by the [visual molecular dynamics (vmd)](http://www.ks.uiuc.edu/Research/vmd/) package. Convert these files to the native [iffi](iffi) input format by the [xpl2lis](xpl2lis) tool.
+
+4. Control File
+------
+The [control file](control file) _ctl.xml_ contains the full set of input options and their default settings.
+

Getting started modified by Gerald Mathias

Gerald Mathias — Wed, 27 Aug 2014 17:13:19 -0000

--- v1
+++ v2
@@ -19,5 +19,5 @@

 2. Compile 
 -----
-Follow the [compiling] instructions. If in doubt, run the [Test Suite] to verify your executable.
+Follow the [compiling](Compiling) instructions. If in doubt, run the [Test Suite] to verify your executable.

Getting started modified by Gerald Mathias

Gerald Mathias — Wed, 27 Aug 2014 17:12:09 -0000

Welcome to the Iphigenie molecular dynamics (MD) simulation program.
To get started follow these steps

1. Download the files provided for the latest version of Iphigenie.

Each version subdirectory contains tared and gziped files that can be expanded

tar -xzpvf <filename>

from a common directory.
Both 'program' and 'share' files are definately needed. 'examples' are useful to get an idea what iphigenie provides and how the various features have to be oparated. The latest file 'testsuite' is mainly intended for developers and provides reference output to check if everything runs correctly.

*   __iphigenie-XXX-program.tar.gz__   :   the source code and build system
*   __iphigenie-XXX-examples.tar.gz__  :   input file examples
*   __iphigenie-XXX-testsuite.tar.gz__ :   reference input and output
*   __iphigenie-XXX-share.tar.gz__     :   parameter and data files

2. Compile

Follow the [compiling] instructions. If in doubt, run the [Test Suite] to verify your executable.