[gmx-users] a problem in the energy minimization

[Mark Abraham]

mjduan at smail.hust.edu.cn wrote:
> Dear staff:
> When I do the energy minimization of my system contain a protein, an ATP 
> and water molecules using mdrun, it stopped at 15 steps, and return 
> following messeges:
> 
> 
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+00
>    Number of steps    =         2000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -3.24259e+05 Fmax= 3.22275e+04, 
> atom= 1264
> Step=   14, Dmax= 1.2e-06 nm, Epot=          nan Fmax= 2.96890e+04, 
> atom= 1262
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1
> 
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
> 
> writing lowest energy coordinates.
> 
> Steepest Descents converged to machine precision in 15 steps,
> but did not reach the requested Fmax < 1.
> Potential Energy  = -3.2425944e+05
> Maximum force     =  3.2227543e+04 on atom 1264
> Norm of force     =            nan
> 
> 
> what's wrong with it?

Probably your topology is broken. Minimize your components independently
and see which of them is broken.

Mark