[gmx-users] SHAKE and pbc=full

[leafyoung81-group at yahoo.com]

--- 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). 

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
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> 
> 
>