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

[Yang Ye]

did you use pme_order=8? Before 3.3.1, you shall use 4.

Yang Ye

Adriana Pietropaolo wrote:
> Hi gmx users,
> these are the data with the version 3.2.1, it's all ok:
>
> 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
>
>