AMBER Archive (2004)

Subject: AMBER: About the calculation of non-bond list

From: Wu Lei (wulei_at_biophy.nju.edu.cn)
Date: Sat Jul 10 2004 - 09:21:57 CDT

I have inserted scripts in the "ew_directp.h" or "ew_directe.h" to monitor the non-bond force calculation for certain atom pairs which is not bonded and within the cutoff distance, but found out that they were included in the non-bond list after thousands of steps.

So my question is what are the conditions required to be included in the non-bond list?

As i know, the non-bond atom pairs should be within the cutoff distance, and some atoms are masked out by bonds or bond angles. Any other restrictions?

Thanks!

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