From 57fd9723a5720a62e2a4fcb81413712a8bb693ef Mon Sep 17 00:00:00 2001 From: Oliver Henrich Date: Fri, 19 Jul 2019 12:30:01 +0100 Subject: [PATCH] Added comment on new duplex3 --- examples/USER/cgdna/README | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/examples/USER/cgdna/README b/examples/USER/cgdna/README index 7b05418661..e97910d2e1 100644 --- a/examples/USER/cgdna/README +++ b/examples/USER/cgdna/README @@ -22,6 +22,14 @@ A - C - G - T - A - C - G - T | | | | | | | | T - G - C - A T - G - C - A +/examples/duplex3: +This is basically the duplex1 run with both nucleotide mass and moment +of inertia set to the values of the standalone implementation of oxDNA, +which are M=I=1. To achieve this, the masses were set directly, whereas +the diameter of the ellipsoid in the data file was changed to 3.16227766. +This allows direct comparision of e.g. trajectory data or energies on a +per-timestep basis until numerical noise leads eventually to deviations. + /util: This directory contains a simple python setup tool which creates single straight or helical DNA strands, DNA duplexes or arrays of DNA