[gmx-users] SHAKE and pbc=full

[David van der Spoel]

> > > Here is the bonds definitions:
> > >  2249 2250    1   11.000    265243.3 ; (0,1)
> > >  2249 2251    1    7.778    265243.3 ; (0,2)
> > >  2249 2252    1    7.778    265243.3 ; (0,3)
> > >  2249 2253    1    4.224    265243.3 ; (0,4)
> > >  2249 2254    1   10.575    265243.3 ; (0,5)
> > >  2249 2255    1   10.909    265243.3 ; (0,6)
> > >  2249 2256    1    9.581    265243.3 ; (0,7)
> > >  ...
> > > (There are 28 of them. Bond length is calculated
> > from
> > > the co-ordinates). 
> > Bonds of 11 nm????????????????????
> Yes. That's a coarse-grain model, constructed with 8
> "anchors" and all othere atoms are dummies. 
> > 
Then you're on your own....

Don't make bonds to the dummies, use real vsites instead.
You can also use bonds instead.

-- 
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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