Aligning structures

From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Thu Mar 09 2006 - 21:20:45 CST

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Hi all,
 
 Is there a way to align all the frames of a dynamics calculation using VMD? I know that one can open two or more molecule files and do an alingment on them, but I need to know if I can do this with a dynamics trajectory having 100 frames or more. I need to align all the structures and then calculate RMSD's. Any help will be most appreciated.
 
 Richard
 
Richard L. Wood, Ph. D.
Computational Chemist
Cockeysville, MD 21030
rwoodphd_at_yahoo.com

• Next message: Peter Freddolino: "Re: Aligning structures"
• Previous message: John Stone: "Re: vmd-l: is possible to remove the waterbox before running VMD"
• In reply to: griadi_at_utalca.cl: "Re: is possible to remove the waterbox before running VMD"
• Next in thread: Peter Freddolino: "Re: Aligning structures"
• Reply: Peter Freddolino: "Re: Aligning structures"
• Reply: Marcos Sotomayor: "Re: vmd-l: Aligning structures"
• Reply: Luis Gracia: "Re: Aligning structures"
• Reply: Dong Luo: "Re: Aligning structures"
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