Create schrodinger.md (#119)

* Create schrodinger.md

* add nav entry for new page

---------

Co-authored-by: Kilian Cavalotti <[email protected]>
Co-authored-by: Kilian Cavalotti <[email protected]>

mkdocs.yml

@@ -286,6 +286,7 @@ nav:
           - Spark:           docs/software/using/spark.md
           - MariaDB:         docs/software/using/mariadb.md
           - PostgreSQL:      docs/software/using/postgresql.md
+          - Schrödinger:     docs/software/using/schrodinger.md
           - Quantum Espresso: docs/software/using/quantum-espresso.md
   - Advanced topics:
       - Connection options:  docs/advanced-topics/connection.md

src/docs/schrodinger.md

@@ -0,0 +1,116 @@
+## Introduction
+
+The [Schrodinger][url_schro] software suite is used to simulate and model molecular behavior at the atomic level.  Schrodinger's software tools include molecular dynamics simulations, quantum mechanics calculations, virtual screening and visualization tools.
+
+Stanford Libraries has purchased a site license for the Schrodinger suite.  Please contact Stanford Libraries: [email protected] cc'ing [email protected] if you would like to access Schrodinger on Sherlock.  After we receive confirmation, 
+we will add your faculty sponsor (PI) to the sh_sw-schrodinger Sherlock group.
+
+## Schrodinger on Sherlock
+
+Schrodinger software is loaded with the module command.  To load the current default version:
+
+```bash
+module load chemistry schrodinger
+```
+
+To see all of our versions use the module spider command:
+
+```bash
+$ module spider schrodinger
+```
+
+Once loaded your $SCHRODINGER variable is automatically set and all Schrodinger commands will run.  For example to run the jaguar command:
+
+```bash
+$ jaguar run  -WAIT H20.in
+```
+
+To call the basic Schrodinger run command, just enter:
+
+```bash
+$ run
+```
+
+or glide:
+​
+```bash
+$ glide
+usage: glide_startup.py [options] <input_file>
+glide_startup.py: error: the following arguments are required: input_file
+```
+
+## Example batch submission
+
+Sample [sbatch][url_sbatch] script, requesting 1 CPU, for 10 minutes on the normal partition with default memory:
+
+```bash
+#!/usr/bin/bash
+#SBATCH -o water.%j.out
+#SBATCH -e water.%j.err
+#SBATCH -n 1
+#SBATCH -t 10:00
+#SBATCH -p normal
+# Load required modules
+module load chemistry schrodinger
+# Run Schrodinger, -WAIT is often required
+jaguar run -WAIT H20.in
+```
+
+Input file:
+
+```
+&gen
+&
+&echo
+&
+&zmat
+O       0.0000000000000   0.0000000000000  -0.1135016000000
+H1      0.0000000000000   0.7531080000000   0.4540064000000
+H2      0.0000000000000  -0.7531080000000   0.4540064000000
+&
+```
+
+Save as H2O.in
+
+
+Submit the sbatch script:
+```bash
+$ sbatch water.sbatch
+```
+
+## Maestro GUI
+
+
+For maestro, once you load the Schrodinger module simply call the Maestro GUI with:
+
+$ maestro
+
+
+If you are using a Mac, open the Terminal App and ssh with the -X option:
+
+```bash
+ssh -X <YourSuNetID>@login.sherlock.stanford.edu
+sh_dev -m 16GB
+ml load chemistry schrodinger
+maestro &
+```
+This will launch the Maestro graphical user interface in the background in an sh_dev session with 16GB of memory.  
+
+
+!!! warning GUI's
+Please be aware that GUIs run over a network and X11 can be quite slow and the HPC environment is not best for GUI analysis, it's more ideal for large scale batch job submission and computation.  
+
+
+If you are using a Windows desktop/laptop you will need to use an X11 client like MobaXterm or Xming, see [X11][url_X11] at Stanford for more information.
+
+!!! warning OnDemand shell sessions
+Note that opening an X11/GUI session will not work in a Sherlock OnDemand terminal session.  You will need to use the methods mentioned above, i.e. a standard terminal session with an X11 client.
+
+
+[comment]: #  (link URLs -----------------------------------------------------)
+
+[url_schro]:  //www.schrodinger.com/
+[url_X11]:  //uit.stanford.edu/service/sharedcomputing/moreX
+[url_sbatch]:      //docs/user-guide/running-jobs/#batch-jobs
+[url_support]:          mailto:{{ support_email }}
+[comment]: #  (footnotes -----------------------------------------------------)