[gmx-users] SHAKE and pbc=full

[leafyoung81-group at yahoo.com]

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> 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????????????????????
Yes. That's a coarse-grain model, constructed with 8
"anchors" and all othere atoms are dummies. 
> 
> 
> > 
> > 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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> > > 
> > > 
> > > 
> > 
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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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> 
> 
>