[gmx-users] Fatal error when using Hbond restraints

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 17 19:53:49 CET 2007

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
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

try using
constraints = all-bonds,
or make sure that your charge groups overlap with the constraint groups.

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

More information about the gromacs.org_gmx-users mailing list