[gmx-users] LINCS warning involving hydrogen

[Perttu Niemelä]

Dear Gromacs users,

There is a thread from July 2003 concerning LINCS errors when simulating
lipids with OH-groups (see message below). I ran into exactly similar
problems and was wondering if anyone has found another solution to this?

The problem is that we would like to study the dynamics of hydrogen
bonding, so the suggested methods (dummy hydrogens, increasing the mass of
hydrogens, etc) do not seem very well applicable.

Is it possible to do some kind of multiple time step run with GROMACS,
treating only hydrogens with very short time step?

Best Regards,

Perttu Niemelä


On Tue, Jul 29 2003, 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
>     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
>