[gmx-users] Shake block error:

David van der Spoel spoel at xray.bmc.uu.se
Mon May 17 08:54:51 CEST 2004

On Mon, 2004-05-17 at 07:33, Ben Roberts wrote:
> Hello all,
> I'm trying to run a simulation and short dynamics run to get a
> relatively equilibrated structure for a molecule.
> The simulation is unusual because it is a highly branched molecule, and
> I have modified the .itp file to repel the ends of the branches both
> from the centre and from each other (in order to generate a completely
> extended structure). This was done via a Type 6 bond, with a very long
> length (I'm aware that a Type 6 bond is a simple harmonic restraint).
> The first stage, running Editconf, Grompp and Mdrun (Energy
> Minimisation) works fine. However, when I try and run Grompp a second
> time in preparation for the dynamics run, I get the following message:
> 	Walking down the molecule graph to make shake-blocks
> 	There are 132 charge group borders and 1 shake borders
> 	There are 132 total borders
> 	Division over nodes in atoms:
>      		187     188
> 	Fatal error: Shake block crossing node boundaries
> 	constraint between atoms (174,203)

the fact that you get this message means that shake is turned on
(constraints = all-bonds) in the mdp file. Using constraints = h-bonds
would make it possible, but then your time step is limited to 1 fs. As
regards the atom numbers in the error message, you have to add 1 to
them, so they correspond to atoms 175 and 204 in your coordinate file. 

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://xray.bmc.uu.se/~spoel

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