[gmx-users] Minimization problem

liu xin zgxjlx at gmail.com
Mon Dec 12 12:33:09 CET 2005

Hello everyone,

I checked the output energy, after SD minimization with my lipid/protein
system, found the value is abnormal:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 2000.
Potential Energy  =            nan
Maximum force     =            inf on atom 9614
Norm of force     =            nan

Then I checked the em.log line by line, found there are two message:

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 2000

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)

Infact I did set "constraints = none" in mdp file, and I got the same
resulte when changing the stepsize from 0.002 to 0.02. Why I got Potential
Energy = nan after SD? What does it mean?
I dont know how to over come this problem, could anybody give me some

Thanks in advance!
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