diff --git a/MPI/NAMD/README.md b/MPI/NAMD/README.md new file mode 100644 index 0000000..c4ed360 --- /dev/null +++ b/MPI/NAMD/README.md @@ -0,0 +1,8 @@ +NAMD +---- + +This directory (and /opt/psi/MPI/NAMD) is reserved for a future compiled version of NAMD. + +We currently use pre-compiled binaries. These are located in Tools/NAMD. + + diff --git a/Tools/NAMD/README.md b/Tools/NAMD/README.md new file mode 100644 index 0000000..d7a5ebe --- /dev/null +++ b/Tools/NAMD/README.md @@ -0,0 +1,23 @@ +NAMD +---- + +NAMD uses a non-commercial license. A disclaimer is printed when the module is loaded. + +Installation +============ + +[Release Notes](https://www.ks.uiuc.edu/Research/namd/cvs/notes.html) + +1. A NAMD account is needed to download binaries +2. Create new directory `/opt/psi/MPI/NAMD/$VERSION` +3. Download the latest binary. + - Use `NAMD_$VERSION_Linux-x86_64-ibverbs-smp-CUDA.tar.gz` +4. Unpack to the new directory with `tar -xzvf NAMD*.tar.gz --strip-components=1 -C /opt/psi/MPI/NAMD/$VERSION` +5. Clean up: + + mkdir bin + find . -maxdepth 1 -executable -type f -exec mv '{}' bin ';' + +6. Add new variant to files/variants +7. Run the build-script to install the modulefile and to set the release + diff --git a/Tools/NAMD/build b/Tools/NAMD/build new file mode 100755 index 0000000..1ec63e1 --- /dev/null +++ b/Tools/NAMD/build @@ -0,0 +1,22 @@ +#!/usr/bin/env modbuild + +# Binary distribution with manual installation. See README.md + +pbuild::add_to_group 'Tools' + +pbuild::prep() { + : +} + +pbuild::configure() { + : +} + +pbuild::compile() { + : +} + +pbuild::install() { + : +} + diff --git a/Tools/NAMD/files/variants b/Tools/NAMD/files/variants new file mode 100644 index 0000000..4cf6851 --- /dev/null +++ b/Tools/NAMD/files/variants @@ -0,0 +1 @@ +NAMD/2.13 unstable diff --git a/Tools/NAMD/modulefile b/Tools/NAMD/modulefile new file mode 100644 index 0000000..68aa534 --- /dev/null +++ b/Tools/NAMD/modulefile @@ -0,0 +1,34 @@ +#%Module1.0 + + +set disclaimer {NAMD is available for Non-Commercial Use only. Before using, please review the +license (http://www.ks.uiuc.edu/Research/namd/license.html). You should also +acknowledge the developers: + + "NAMD was developed by the Theoretical and Computational Biophysics Group + in the Beckman Institute for Advanced Science and Technology at the + University of Illinois at Urbana-Champaign." + +And cite the reference: + + James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad + Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant + Kale, and Klaus Schulten. Scalable molecular dynamics with NAMD. Journal of + Computational Chemistry, 26:1781-1802, 2005. abstract, journal + +And link the website: http://www.ks.uiuc.edu/Research/namd/} + +module-whatis "Scalable Molecular Dynamics Software" +module-url "http://www.ks.uiuc.edu/Research/namd/" +module-license "NAMD Non-Commercial License (http://www.ks.uiuc.edu/Research/namd/license.html)" +module-maintainer "Spencer Bliven