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
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