[gmx-users] DUMMY and CONSTRAINED

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 21 11:35:02 CEST 2004

On Wed, 2004-04-21 at 09:53, acorrea at unisa.it wrote:
> Hallo.
> I would like to performe a all-bonds constrain molecular dynamics, (I think with
>  shake) but I have dummy atoms in my sistems and I must define bonds respect
> these dummy atoms. 
> If I put in a file.mdp :
> constrained = all-bonds
> constraint-algorithm     = Shake
> in the compilation step I found (atoms 27 and 28 are two dummy atoms):
> double-checking input for internal consistency...
> Cleaning up constraints and constant bonded interactions with dummy particles
> ERROR: Cannot have constraint (1-27) with dummy atom (27)
> ERROR: Cannot have constraint (11-28) with dummy atom (28)

Did you make the topology yourself?
There is an option -normdumbds in grompp that you could try. If it
doesn't work send the relevant bit of the topology to the list.

By the way, do check the resulting tpr file (gmxdump -s)
David van der Spoel, PhD, Assist. 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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