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

[David van der Spoel]

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.

> 
> 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
> 


-- 
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://folding.bmc.uu.se
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