[gmx-users] Unable to minimize energy

[Mark Abraham]

Paul Whitford wrote:
> This is likely an embarrassingly trivial problem, but let's see.
> 
> I am following the energy minimization scheme presented in the groningen 
> tutorial
> 
> http://md.chem.rug.nl/education/mdcourse/MDpract.html
> 
> I believe I follow the directions exactly, yet I can not minimize below 
> Fmax~500

I did the tutorial as written and got

"...
Step=  115, Dmax= 1.3e-06 nm, Epot= -1.07212e+04 Fmax= 1.46265e+03, 
atom= 775
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 116 steps,
but did not reach the requested Fmax < 1.
Potential Energy  = -1.0721238e+04
Maximum force     =  1.5431615e+03 on atom 775
Norm of force     =  9.6257832e+03"

Thus I'd say you've done OK. Ultimately, if the EM prepares a structure 
well enough that the equilibration phase of the MD works, then that's 
good enough.

Mark