From 39a31514d34f69402ac73cc4fda14b4fde2b5bb8 Mon Sep 17 00:00:00 2001 From: Mark Piercy Date: Mon, 11 Sep 2023 14:06:13 -0700 Subject: [PATCH] Update schrodinger.md (#120) * Create schrodinger.md * add nav entry for new page * Update schrodinger.md fix typos * fixes for spellcheck test --------- Co-authored-by: Kilian Cavalotti Co-authored-by: Kilian Cavalotti --- .github/workflows/config/spellcheck.wordlist.txt | 2 ++ src/docs/software/using/schrodinger.md | 14 +++++++------- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/.github/workflows/config/spellcheck.wordlist.txt b/.github/workflows/config/spellcheck.wordlist.txt index 3cc6f3dd4..3568e2cf9 100644 --- a/.github/workflows/config/spellcheck.wordlist.txt +++ b/.github/workflows/config/spellcheck.wordlist.txt @@ -18,3 +18,5 @@ MPI NUMA PDU SMP +Schrödinger +OnDemand diff --git a/src/docs/software/using/schrodinger.md b/src/docs/software/using/schrodinger.md index a8bfa214a..33b5a3e6f 100644 --- a/src/docs/software/using/schrodinger.md +++ b/src/docs/software/using/schrodinger.md @@ -2,7 +2,7 @@ The [Schrödinger][url_schrodinger] suite is a commercial and licensed software used to simulate and model molecular behavior at the atomic level. -Schrödinger's software tools include molecular dynamics simulations, quantum +The Schrödinger software tools include molecular dynamics simulations, quantum mechanics calculations, virtual screening and visualization tools. ### More documentation @@ -19,11 +19,11 @@ contact [Schrödinger support][url_schrodinger_support]. [Stanford Libraries][url_sul] have purchased a site license for the Schrödinger suite. Please contact Stanford Libraries at sciencelibrary@stanford.edu and CC {{ support_email }} if you would like to access Schrödinger on Sherlock: after -we receive confirmation, your PI group will be granted access. on Sherlock. +we receive confirmation, your PI group will be granted access on Sherlock. ### Using Schrödinger -You can use Schrödinger software fater having loaded the corresponding +You can use Schrödinger software after having loaded the corresponding [software module][url_modules] with the `module` command. To load the current default version: @@ -77,7 +77,7 @@ $ maestro ``` You'll need to enable X11 forwarding in your initial connection to Sherlock, -and request it as well for your job allocationi. +and request it as well for your job allocation. Here are some example commands you can run: @@ -104,15 +104,15 @@ interface on your local machine's display. scheduled computations are carried over on the cluster. -For more information about X11 forwarding, you can refer to this [UIT -page][url_x11]. +For more information about X11 forwarding, you can refer to this +[page][url_x11]. ## Examples ### batch job submission -Here's an example [sbatch][url_sbatch] script, requesting 1 CPU, for 10 minutes +Here's an example [batch][url_sbatch] script, requesting 1 CPU, for 10 minutes on the `normal` partition, that can be saved as `water.sbatch`: ```bash