AMBER Archive (2006)

Subject: AMBER: another question: is rms 2E-2 good for nmode ntrun=1?

From: Pan, Yongmei (
Date: Fri May 12 2006 - 10:22:00 CDT

Hi, guys
another question for starting structure for nmode ntrun=1. After 10000 cycles of GB(igb=2) follwed by 10000 cycles of epsilon=4r sander minimization, the rms wandered around 2E-2, and it seems that it would take forever to reach E-3 magnitude. Is this because my molecule with 6420 atoms is too big to reach a small rms? and if the rms cannot be smaller, is rms value 2E-2 small enough for the nmode ntrun=1 calculation?
Thanks in advance
Yongmei Pan
College of Pharmacy, University of Kentucky
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