From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Mon Aug 09 2010 - 03:13:58 CDT
On Monday 09 August 2010 09:28:16 you wrote:
> Hi everyone,
> I'm new to NAMD. While I energy minimized my system, I got a warning as
> below in the log file:
> Warning: Ignored 12 bonds with zero force constants.
> Can anyone tell me what does that mean and how it may affect my simulation?
I guess you are using the TIP3 Water model with SHAKE and probably have 12
Water molecules in your system?
If this is correct, you don't have to worry about the Warning.
-- Bjoern Olausson Martin-Luther-Universitšt Halle-Wittenberg Fachbereich Biochemie/Biotechnologie Kurt-Mothes-Str. 3 06120 Halle/Saale Phone: +49-345-55-24942
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