VMD-L Mailing List

From: Kara Di Giorgio (kdigiorgio_at_sbcglobal.net)
Date: Tue Nov 15 2005 - 19:43:35 CST

I know this is not exactly a VMD question, but I though the community
may have run across this question before.

Does anyone know of a method to quantify how much DNA has been
perterbed during a MD run? I have done MD simulations of DNA with a
cross-linker of various lengths in it. I need to compare how much each
linker perterbed the DNA. Does anyone have any ideas?

Thank you,

Kara Di Giorgio