[gmx-users] SHAKE and pbc=full

[David van der Spoel]

On Thu, 2005-09-08 at 07:06 -0700, leafyoung81-group at yahoo.com wrote:
> 
> --- David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 
> > 
> > > > > 
> > > > Increase the number of exclusions.
> > 
> > > Exclusion is considered and put into the
> > energy_excl
> > > group.
> > > > 
> > I mean in your molecule definition, use:
> > [ moleculetype ]
> > ; NAME	nrexcl
> > Mymol	4
> > (or higher)
> 
> I have tried but still failed. Actually, the explosion
>  is not caused by non-bonded interactions.
> 
> Here is the coordinates
>     1SPD     A1 2249  17.500  11.000  12.798
>     1SPD     A2 2250   6.500  11.000  12.798
>     1SPD     A3 2251  12.000  16.500  12.798
>     1SPD     A4 2252  12.000   5.500  12.798
>     1SPD     A5 2253  16.272   7.536  14.881
>     1SPD     A6 2254   7.728  14.464  10.715
>     1SPD     A7 2255   7.076   8.550  14.881
>     1SPD     A8 2256   9.550   6.076  10.715
> 
> 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????????????????????


> 
> After step -3 and step -2, at step -1 LINCS gives
> 
> Step -1, time -0.01 (ps)  LINCS WARNING
> relative constraint deviation after LINCS:
> max 5056.670666 (between atoms 9257 and 9265) rms
> 638.613072
> bonds that rotated more than 30 degrees:
>  atom 1 atom 2  angle  previous, current, constraint
> length
>    2249   2250  174.0    9.5164 155.6892     11.0000
>    2249   2251   50.4   21.5753 106.3830      7.7780
>    2249   2252   44.7   21.5742 135.9422      7.7780
>    2249   2253  143.2   11.7016 124.8937      4.2240
> ...
> 
> > 
> > -- 
> > 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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-- 
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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