From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-chemistry/pdbmat/metadata.xml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 sci-chemistry/pdbmat/metadata.xml (limited to 'sci-chemistry/pdbmat/metadata.xml') diff --git a/sci-chemistry/pdbmat/metadata.xml b/sci-chemistry/pdbmat/metadata.xml new file mode 100644 index 000000000000..d542eb59e001 --- /dev/null +++ b/sci-chemistry/pdbmat/metadata.xml @@ -0,0 +1,24 @@ + + + + sci-chemistry + + jlec@gentoo.org + + +A fortran program in which Tirion's model (also called the Elastic Network +Model) is implemented. Within the frame of this model, atoms (particles) +less than cutoff (angstroms) away from each others are linked by springs of +same strength. Alternatively, a list of interacting atoms can be given to the +program. +Requirements: a file with the coordinates of the system, in PDB (Protein Data +Bank) or "x y z mass" format. + +Output: the hessian (the mass-weighted second derivatives of energy matrix), +in the "i j non-zero-ij-matrix-element" format. + +Diagstd, a fortran program with a standard diagonalization routine, can next +be used in order to obtain the corresponding normal modes of the system. If +the system is large, the RTB approximation can prove usefull (see below). + + -- cgit v1.2.3-65-gdbad