[gmx-users] Fatal error when using Hbond restraints

[David van der Spoel]

Robert Johnson wrote:
> Hello everyone,
> I'm performing a simulation that includes a 2D infinite SiO2
> substrate. I'm not interested in the high frequency motion of the
> substrate bonds, so I'm applying position restraints to all the SiO2
> atoms. I have other molecules in the system such as water and DNA that
> require hydrogen bond restraints. However, I'm getting the following
> error when trying to run the system across several nodes:
> Fatal error:
> Shake block crossing node boundaries
> constraint between atoms (1680,1716)
> 
> The atoms listed are in the substrate. Since I'm already restraining
> the substrate atoms, I don't really need to constrain the Hbonds in
> the SiO2. Is there any way to apply Hbond restraints only to a group
> of atoms?
> 
> Alternatively, how does Gromacs decide which bonds contain hydrogen? I
> could just alter the topology file for the substrate to trick Gromacs
> into thinking that the hydrogens in the SiO2 are really a different
> type of atom.
> Thanks,
> Bob Johnson
I'm at this very moment looking at 
http://bugzilla.gromacs.org/show_bug.cgi?id=110
which reports the same error. You might try to use pbc=full and 
contraint_algorithm = lincs to circumvent the problem.

The problem you have does not arise from the position restraints though, 
and, by the way, you probably don't need those restraints at all. I 
don't know what you mean with hbond restraints though...

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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