[gmx-users] How to circumvent shake-block errors ?

David van der Spoel spoel at xray.bmc.uu.se
Fri Dec 14 09:17:03 CET 2001

On Fri, 14 Dec 2001, Marc Baaden wrote:

>just came across an error I hadn't seen before ...
>looks like this:
>Walking down the molecule graph to make shake-blocks
>There are 4228 charge group borders and 1 shake borders
>There are 4228 total borders
>Division over nodes in atoms:
>  3633  3634
>Fatal error: Shake block crossing node boundaries
>constraint between atoms (3632,3637)
>I can see that there might be a problem splitting a constrained
>bond over 2 processors .. is there a way to cricumvent this ?
>(I have only 1 molecule in my simulation).
That's corrected. It simply isn't implemented. One option you have is to
use constraints only for the hydrogens and use flexible bonds for the
heavy atoms.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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