[gmx-users] a problem in the energy minimization
Mark.Abraham at anu.edu.au
Tue Aug 14 17:08:44 CEST 2007
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.
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