[gmx-users] Energy Minimisation and Equilibration Problems

[Mark Abraham]

Nancy wrote:
> I ran the minimisation, and mdrun gave the following last few lines of
> output:
> 
> ==================================
> Step=19990, Dmax= 7.8e-06 nm, Epot= -7.14922e+04 Fmax= 3.19585e+04, atom=
> 2395
> Step=19992, Dmax= 4.7e-06 nm, Epot= -7.14924e+04 Fmax= 8.72456e+03, atom=
> 2395
> Step=19993, Dmax= 5.6e-06 nm, Epot= -7.14927e+04 Fmax= 3.70693e+04, atom=
> 2395
> Step=19994, Dmax= 6.8e-06 nm, Epot= -7.14929e+04 Fmax= 2.10513e+04, atom=
> 2395
> Step=19995, Dmax= 8.1e-06 nm, Epot= -7.14929e+04 Fmax= 4.71234e+04, atom=
> 2395
> Step=19996, Dmax= 9.7e-06 nm, Epot= -7.14931e+04 Fmax= 3.68827e+04, atom=
> 2395
> Step=19998, Dmax= 5.8e-06 nm, Epot= -7.14933e+04 Fmax= 1.35461e+04, atom=
> 2395
> Step=19999, Dmax= 7.0e-06 nm, Epot= -7.14933e+04 Fmax= 4.77130e+04, atom=
> 2395
> Step=20000, Dmax= 8.4e-06 nm, Epot= -7.14936e+04 Fmax= 2.41860e+04, atom=
> 2395
> 
> writing lowest energy coordinates.
> 
> Steepest Descents did not converge to Fmax < 10 in 20001 steps.
> Potential Energy  = -7.1493609e+04
> Maximum force     =  2.4185994e+04 on atom 2395
> Norm of force     =  8.1511212e+02
> ==================================
> 
> As you can be seen, the forces still do not converge to Fmax < 10, even
> after 20,000 steps.
> 
> Does anyone know what the problem might be?

No. You have to look at the structure and the simulation box and see if 
there's anything unrealistic. That's tedious and time-consuming, but if 
you're aware there's a problem, you need to do that.

Mark