[gmx-users] a problem about the minimization

[Mark Abraham]

zhuliang at tju.edu.cn wrote:
> Hi all:
>    When I performed a steepest minimization, a problem occured and the error
> message pasted here:
> "  Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+04
>    Number of steps    =       100000
> Step=   13, Dmax= 1.2e-06 nm, Epot=          nan Fmax= 4.96310e+14, atom= 2191
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 10000 "
> 
> Double precision normally gives you higher accuracy
> 
> I have changed the emstep, but the same error message occured again. can you give
> me some advise to deal with it. Thank you in advance!

A "nan" potential energy and a massive positive maximum force indicate 
that your system is badly broken. Varying the size of the EM step, or 
the number of steps won't help this. Check your starting structure, your 
topology, any warnings from grompp. Visualize the structure, and or the 
minimization trajectory to see where things are falling apart.

Mark