[gmx-users] LINCS WARNING...

[David]

On Tue, 2003-07-29 at 20:18, Senthil Kandasamy wrote:
> 
> > _____________________________________________
> > Step 400, time 0.8 (ps)  LINCS WARNING
> > relative constraint deviation after LINCS:
> > max 0.120018 (between atoms 334 and 335) rms 0.002054
> > bonds that rotated more than 30 degrees:
> >  atom 1 atom 2  angle  previous, current, constraint length
> >     333    335   33.8    0.2081   0.2040      0.2000
>                                                 ^^^^^^
> It seems like you are running with constraints = all-angles
> LINCS is not good at this. Your options are to use shake for the
> constraint algorithm or use constraints = all-bonds


> ___________________
> 
> 
> David, 
> 
> I had tried all-bonds and also tried the SHAKE algorithm earlier. They
> all seem to crash and the culprit always seems to be that one particular
> hydrogen atom. Is there any other way to make it stable? 
> 
Maybe there is a strong interaction between the hydrogen and a 1-4 atom?
Otherwise, is the hydrogen solvated or hydrogen bonded in any way?
What's the charge on the hydrogen?



> Senthil
>     
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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