[gmx-users] LINCS warning involving hydrogen

[David]

On Tue, 2003-07-29 at 19:34, Senthil Kandasamy wrote:
> Hi all, 
> 
> I have a glycerol headgroup for a lipid and I am running into LINCS
> warnings during a short md run which eventually crashes.
> 
> structure:
> 
> H-O-CH2-CH-O-H
>          |
>          CH2-......lipid
> 
> as united atoms:
> 
> H-O-C-C-O-H
>       |
>       C-......lipid
> 
> this is the warning I get :
> _____________________________________________
> 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

    
>     334    335   72.2    0.1297   0.1120      0.1000
>    4311   4313   36.0    0.2086   0.1984      0.2000
>    4312   4313   78.1    0.1089   0.1081      0.1000
>    6147   6149   37.1    0.2184   0.1979      0.2000
>    6148   6149   75.7    0.1187   0.1077      0.1000
> ____________________________________________________
> 
> 335, 4313 and 6149 are hydrogen atoms attached to the -CH-O- moiety.
> 333  4311 and 6147 are the carbon atoms of the -CH-O-H and 
> 334  4312 and 6148 are the oxygen atoms of the -CH-O-H.
> 
> What would prevent this hydrogen atom from moving around so much? How
> can I constrain it? Some earlier posts, mention something about the
> pairs directive. Should I remove all the pairs involving that hydrogen?
> I am a bit confused. 
> 
> (I had created the topology file using prodrg for this molecule and then
> edited it )
> 
> 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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