[gmx-users] Shake block error:

[David van der Spoel]

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.
________________________________________________________________________
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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