base stacking analysis of the trajectory of a nucleic acids simulation

From: Tianjiao Wang (
Date: Tue Dec 30 2008 - 15:54:31 CST

Dear all,

  I have finished a molecular dynamics simulation of a small RNA by NAMD 2.6.
I am wondering whether there is a way to quantify the occupancy of base
stackings between residues from the MD trajectory. Thank you very much for
your advice and happy holiday!


Tianjiao Wang
3288 MBB
Iowa State Univ
Ames, IA 50010

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