[gmx-users] gromacs 4.6 GB/SA problem and poor performance

[Roland Schulz]

On Mon, Jan 21, 2013 at 3:55 AM, Changwon Yang <sht_ycw79 at hotmail.com>wrote:

> Im trying to run an md or em using an implicit solvation method using
> gromacs 4.6 but I always get the incorrect result.
> ICC version : icc 11.0
>  fftw version : 3.2.2
>
> benchmark system is gromacs-gpubench
> gromacs-gpubench-dhfr.tar/CPU/dhfr-impl-inf.bench
>
> Angle,Proper Dih,Imp Dih,Nonpolar sol,LJ-14,Coulomb-14 energy are correct.
> but GB polarization energy is too low, LJ(SR),Coulomb(SR) energy are always
> zero.
>
>
>
> It seems that there is a bug in the program.
>
> Using gromacs 4.5. It works fine.
>
> gromacs 4.5.3 : 9.4ns/day
> gromacs 4.6 :2.4ns/day
>

Please provide the output of "mdrun -version". Also ICC 11.0 is quite old.
Please test whether the same issue is present with a more recent ICC or GCC
compiler.

Roland


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