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.
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