[gmx-users] more detailed problem from 3.2.1 to 3.3 version

[Adriana Pietropaolo]

On Wed, 8 Mar 2006, David van der Spoel wrote:

> Adriana Pietropaolo wrote:
> > Hi gmx users,
> > these are the data with the version 3.2.1, it's all ok:
> 
> Is this the first step of the simulation? Not likely since all energies 
> are different... If not what is it? Have you compared tpr files with 
> gmxcheck? If you have a tpr file that works fine in 3.2.1 but not in 3.3 
> the please upload a bugzilla.gromacs.org entry for it.
> 

yes, they are both the first step,
anyway I'll try your advise for the gmxcheck...
it's very strange,
thanks anyway,
Adriana

> > 
> > Grid: 10 x 14 x 17 cells
> > There are 83733 atoms in your xtc output selection
> >    Energies (kJ/mol)
> >            Bond          Angle    Proper Dih. Ryckaert-Bell.          
> > LJ-14
> >     7.44899e+03    8.75680e+03    4.31061e+02    3.28696e+03    
> > 5.39252e+03
> >      Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb 
> > (LR)
> >     2.48117e+04    1.80599e+05   -5.61322e+03   -1.17685e+06   
> > -1.90115e+05
> >       Potential    Kinetic En.   Total Energy    Temperature Pressure 
> > (bar)
> >    -1.14185e+06    2.13932e+05   -9.27915e+05    3.00030e+02   
> > -7.15918e+01
> > 
> > while these with 3.3:
> > Grid: 10 x 14 x 17 cells
> > Configuring nonbonded kernels...
> > Testing ia32 SSE2 support... present.
> > 
> > 
> > There are 83733 atoms in your xtc output selection
> >    Energies (kJ/mol)
> >            Bond          Angle    Proper Dih. Ryckaert-Bell.          
> > LJ-14
> >     7.10625e+03    8.40265e+03    4.76377e+02    3.35038e+03    
> > 5.43981e+03
> >      Coulomb-14        LJ (SR)        LJ (LR)   Coulomb (SR)   Coul. 
> > recip.
> >     2.48765e+04    1.82369e+05   -5.61075e+03   -1.17885e+06   
> > -1.88813e+05
> >       Potential    Kinetic En.   Total Energy    Temperature Pressure 
> > (bar)
> >    -1.14125e+06    2.16886e+05   -9.24363e+05    3.04173e+02    
> > 1.07877e+02
> > 
> > Large VCM(group rest):      0.00110,      0.00115, ...etc...
> > since telling that:
> > 
> > Grid: 13 x 18 x 22 cells
> > WARNING: your box is exploding! (ncells = 5148)
> > Large VCM(group rest):      0.00120,      0.00111,      0.00112, ekin-cm:  
> > 1.00291e+00
> > 
> > 
> > why this in your opinion?
> > the input is the same
> > is there a problem with barostat and temperature?
> > I used berendsen in all the same...
> > thanks,
> > Adriana
> > 
> 
> 
> 

-- 
_____________________________________________
Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
WEB:www2.fci.unibo.it/~adriana
Tel 051/6446992
FAX 051/2093690 
_____________________________________________