base stacking analysis of the trajectory of a nucleic acids simulation

From: Tianjiao Wang (tjwang_at_iastate.edu)
Date: Tue Dec 30 2008 - 15:54:31 CST

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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

Tianjiao Wang
3288 MBB
Iowa State Univ
Ames, IA 50010
e-mail: tjwang_at_iastate.edu

• Next message: sunita gupta: "How to get over with the error "Atoms moving too fast; simulation has become unstable and Exiting prematurely."
• Previous message: Axel Kohlmeyer: "Re: compiling NAMD failed on windows with Cygwin"
• Next in thread: Chris Harrison: "Re: base stacking analysis of the trajectory of a nucleic acids simulation"
• Reply: Chris Harrison: "Re: base stacking analysis of the trajectory of a nucleic acids simulation"
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