AMBER: how to average the structure along md trajectory

From: Ye Mei <>
Date: Wed, 6 Jul 2005 21:51:56 +0800

Dear amber users

I wanna try to average the md trajectory and compare it with x-ray crystal structure. I tried average keyword in ptraj module. But the averaged structure has shorter bond length. This can be explained if one tries to average the structure by cartesian coordinates. For example, the average structure of spinning water molecule in only one point. Is there anyway to average the trajectory but keep the bond length?
Best regards,

Ye Mei
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093

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Received on Wed Jul 06 2005 - 15:53:01 PDT
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