Re: constraint failure in RATTLE algorithm for atom 3205

From: Schreiner Eduard (
Date: Fri Nov 14 2008 - 20:13:30 CST

Well, as you said, there seem to be some atoms to close to each other.
Besides, without any additional information, like the time step used, it
is difficult to say something useful.
Maybe you want to check your structure after the minimization,
although 100000 steps should optimize the structure sufficiently, as
long as it isn't a pathological case.
However, I do not think, it's a bug, but rather maybe something is not
quite right with
your setup/structure


On Nov 14, 2008, at 7:42 PM, ydhuang2727 wrote:

> Hi,
> everyone,
> please have a look at the following:
> minimize 100000
> run 10000000 ;# 10ns
> NAMD stopped at 100000, right after minimizing.
> and i got an error:
> constraint failure in RATTLE algorithm for atom 3205 or 3188.
> constraint failure ;simulation has become unstable.
> It should be pointed out that the two atoms are both close to the
> ligand molecule of the protein and this error didn't occur when i
> used the protein alone, so i guess it is due to the existing of the
> ligand in the protein.
> I have no idea at what situation such a bug comes about, this is
> what i badly want to know!
> Thanks for your kind consideration and look forward to your quick
> reply!
> Bless!
> dong,
> [广告] 金秋最关注楼盘-房不胜房

Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078

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