bad exclusion error - searching remedies

From: Arturas Ziemys (
Date: Mon Aug 18 2008 - 18:12:48 CDT


I came across the problem I can not solve and understand.
I have an amorphous silica slab (8x8nm). I have applied bonding across
boundary to images to mimic infinite layer. I successfully minimized
silica(fixed or constrained)+water system and do plain MD well. However,
I modified that silica slab by attaching -OH groups and can not get rid
from "bad exclusion" errors:

Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global bond count!
Warning: Bad global angle count!

I checked the troubleshooting of NAMD. I can not find the reason why it
happens that all my minimizations retain errors even minimizing slab -OH
groups alone. I do not have hydrogen bonds for example. I have modified
-OH group position that those would cross system boundary too much in
start-up structure. I used to simulate silica system full of -OH of
twice smaller dimension without any problems at all. I did several
different preparation of my slab system - the same.

Please - any comments.


Arturas Ziemys, PhD
  School of Health Information Sciences
  University of Texas Health Science Center at Houston
  7000 Fannin, Suit 880
  Houston, TX 77030
  Phone: (713) 500-3975
  Fax:   (713) 500-3929  

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