From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
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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