about recentering of namd trajectory

From: zhangliqun (lqzhang0332_at_hotmail.com)
Date: Tue Aug 17 2010 - 10:50:54 CDT

Dear NAMD administrator:

I ran protein complex simulations (one protein with one small gtpase) using NAMD software. In the input file, I used wrapall on settings. In analyzing the rmd based on the trajectory, I found very large values of msd for the complex after align the frame orientation to the initial position. I tried to use chamm code to do recentering on the trajectory, but no improvement. Could you give me some idea on how to solve that? Thank you very much.

Best regards,

Liqun Zhang

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